<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_11_0/emdb.xsd" version="3.0.11.0" emdb_id="EMD-18652">
    <admin>
        <current_status>
            <date>2025-07-02</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2024-10-23">
                <change_list>
                    <fsc>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </fsc>
                    <half_map part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <half_map part="2">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <mask>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </mask>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
            <revision version="2.0" date="2024-11-06">
                <change_list>
                    <model>
                        <revision_group>STRUCTURE_SUMMARY</revision_group>
                        <categories>
                            <category>atom_site</category>
                            <category>citation</category>
                            <category>em_admin</category>
                            <category>entity</category>
                            <category>entity_name_com</category>
                            <category>entity_poly</category>
                            <category>entity_poly_seq</category>
                            <category>entity_src_gen</category>
                            <category>pdbx_entity_nonpoly</category>
                            <category>pdbx_modification_feature</category>
                            <category>pdbx_nonpoly_scheme</category>
                            <category>pdbx_poly_seq_scheme</category>
                            <category>pdbx_struct_sheet_hbond</category>
                            <category>pdbx_unobs_or_zero_occ_residues</category>
                            <category>struct_asym</category>
                            <category>struct_conf</category>
                            <category>struct_conn</category>
                            <category>struct_ref</category>
                            <category>struct_ref_seq</category>
                            <category>struct_sheet_range</category>
                        </categories>
                        <items>
                            <item>_atom_site.label_entity_id</item>
                            <item>_atom_site.label_seq_id</item>
                            <item>_citation.pdbx_database_id_DOI</item>
                            <item>_citation.year</item>
                            <item>_em_admin.last_update</item>
                            <item>_entity_name_com.entity_id</item>
                            <item>_pdbx_entity_nonpoly.entity_id</item>
                            <item>_pdbx_modification_feature.label_seq_id</item>
                            <item>_pdbx_modification_feature.modified_residue_label_seq_id</item>
                            <item>_pdbx_nonpoly_scheme.entity_id</item>
                            <item>_pdbx_struct_sheet_hbond.range_1_label_seq_id</item>
                            <item>_pdbx_struct_sheet_hbond.range_2_label_seq_id</item>
                            <item>_struct_asym.entity_id</item>
                            <item>_struct_conf.beg_label_seq_id</item>
                            <item>_struct_conf.end_label_seq_id</item>
                            <item>_struct_conn.ptnr1_label_seq_id</item>
                            <item>_struct_conn.ptnr2_label_seq_id</item>
                            <item>_struct_ref_seq.db_align_beg</item>
                            <item>_struct_ref_seq.pdbx_auth_seq_align_beg</item>
                            <item>_struct_ref_seq.ref_id</item>
                            <item>_struct_ref_seq.seq_align_end</item>
                            <item>_struct_sheet_range.beg_label_seq_id</item>
                            <item>_struct_sheet_range.end_label_seq_id</item>
                        </items>
                    </model>
                </change_list>
            </revision>
            <revision version="2.1" date="2024-11-13">
                <change_list>
                    <model>
                        <revision_group>DATA_COLLECTION</revision_group>
                        <categories>
                            <category>em_admin</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                        </items>
                    </model>
                </change_list>
            </revision>
            <revision version="2.2" date="2024-11-20">
                <change_list>
                    <model>
                        <revision_group>DATABASE_REFERENCES</revision_group>
                        <categories>
                            <category>citation</category>
                            <category>citation_author</category>
                            <category>em_admin</category>
                        </categories>
                        <items>
                            <item>_citation.country</item>
                            <item>_citation.journal_abbrev</item>
                            <item>_citation.journal_id_CSD</item>
                            <item>_citation.journal_id_ISSN</item>
                            <item>_citation.title</item>
                            <item>_em_admin.last_update</item>
                        </items>
                    </model>
                </change_list>
            </revision>
            <revision version="2.3" date="2024-11-27">
                <change_list>
                    <model>
                        <revision_group>DATABASE_REFERENCES</revision_group>
                        <categories>
                            <category>citation</category>
                            <category>em_admin</category>
                        </categories>
                        <items>
                            <item>_citation.pdbx_database_id_PubMed</item>
                            <item>_citation.title</item>
                            <item>_em_admin.last_update</item>
                        </items>
                    </model>
                </change_list>
            </revision>
            <revision version="2.4" date="2025-03-26">
                <change_list>
                    <model>
                        <revision_group>DATABASE_REFERENCES</revision_group>
                        <categories>
                            <category>citation</category>
                            <category>citation_author</category>
                            <category>em_admin</category>
                        </categories>
                        <items>
                            <item>_citation.journal_volume</item>
                            <item>_citation.page_first</item>
                            <item>_citation.page_last</item>
                            <item>_citation.year</item>
                            <item>_citation_author.identifier_ORCID</item>
                            <item>_em_admin.last_update</item>
                        </items>
                    </model>
                </change_list>
            </revision>
            <revision version="2.5" date="2025-07-02">
                <change_list>
                    <model>
                        <revision_group>DATA_COLLECTION</revision_group>
                        <categories>
                            <category>em_admin</category>
                            <category>em_software</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                            <item>_em_software.name</item>
                        </items>
                    </model>
                </change_list>
            </revision>
            <revision version="1.1" date="2025-07-02">
                <change_list>
                    <metadata>
                        <revision_group>EXPERIMENTAL_SUMMARY</revision_group>
                        <categories>
                            <category>em_admin</category>
                            <category>em_software</category>
                        </categories>
                        <items>
                            <item>_em_admin.last_update</item>
                            <item>_em_software.name</item>
                        </items>
                    </metadata>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2023-10-12</deposition>
            <header_release>2024-10-23</header_release>
            <map_release>2024-10-23</map_release>
            <update>2025-07-02</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>German Research Foundation (DFG)</funding_body>
                <code>SFB1557</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of the apo yeast Ceramide Synthase</title>
        <authors_list>
            <author>Schaefer J</author>
            <author>Clausmeyer L</author>
            <author>Koerner C</author>
            <author>Moeller A</author>
            <author>Froehlich F</author>
        </authors_list>
        <keywords>Ceramide Synthase, MEMBRANE PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-8163-1629" order="1">Schafer JH</author>
                    <author order="2">Clausmeyer L</author>
                    <author order="3">Korner C</author>
                    <author order="4">Esch BM</author>
                    <author ORCID="0009-0005-0299-8171" order="5">Wolf VN</author>
                    <author ORCID="0009-0004-8681-7085" order="6">Sapia J</author>
                    <author order="7">Ahmed Y</author>
                    <author ORCID="0000-0002-8797-3184" order="8">Walter S</author>
                    <author ORCID="0000-0003-2146-1140" order="9">Vanni S</author>
                    <author ORCID="0000-0002-3279-7590" order="10">Januliene D</author>
                    <author ORCID="0000-0003-1101-5366" order="11">Moeller A</author>
                    <author ORCID="0000-0001-8307-2189" order="12">Frohlich F</author>
                    <title>Structure of the yeast ceramide synthase.</title>
                    <journal_abbreviation>Nat.Struct.Mol.Biol.</journal_abbreviation>
                    <country>US</country>
                    <volume>32</volume>
                    <first_page>441</first_page>
                    <last_page>449</last_page>
                    <year>2025</year>
                    <external_references type="PUBMED">39528796</external_references>
                    <external_references type="DOI">doi:10.1038/s41594-024-01415-2</external_references>
                    <external_references type="ISSN">1545-9985</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>8qtn</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Heterotetrameric complex of yeast ceramide synthase with Lag1, Lac1 and Lip1</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Heterotetrameric complex of yeast ceramide synthase with Lag1, Lac1 and Lip1</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.14</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Ceramide synthase LAG1</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.037150789</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>YREMNYRHSWLTPFFILVCVYSAYFLSGNRTESNPLHMFVAISYQVDGTDSYAKGIKDLSFVFFYMIFFTFLREFLMDVV
IRPFTVYLNVTSEHRQKRMLEQMYAIFYCGVSGPFGLYIMYHSDLWLFKTKPMYRTYPVITNPFLFKIFYLGQAAFWAQQ
ACVLVLQLEKPRKDYKELVFHHIVTLLLIWSSYVFHFTKMGLAIYITMDVSDFFLSLSKTLNYLNSVFTPFVFGLFVFFW
IYLRHVVNIRILWSVLTEFRHEGNYVLNFATQQYKCWISLPIVFVLIAALQLVNLYWLFLILRILYRLI</string>
                    <external_references type="UNIPROTKB">P38703</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Ceramide synthase LAC1</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.036235554999999996</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>FREISYRHAWIAPLMILIAVYSAYFTSGNTTKTNVLHRFVAVSYQIGDTNAYGKGINDLCFVFYYMIFFTFLREFLMDVV
IRPFAIRLHVTSKHRIKRIMEQMYAIFYTGVSGPFGIYCMYHSDLWFFNTKAMYRTYPDFTNPFLFKVFYLGQAAFWAQQ
ACILVLQLEKPRKDHNELTFHHIVTLLLIWSSYVFHFTKMGLPIYITMDVSDFLLSFSKTLNYLDSGLAFFSFAIFVVAW
IYLRHYINLKILWSVLTQFRTEGNYVLNFATQQYKCWISLPIVFVLIGALQLVNLYWLFLIFRVL</string>
                    <external_references type="UNIPROTKB">P28496</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>Ceramide synthase subunit LIP1</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.01544453</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>PKIFNLFRVCFISLLLIAAVEYFKYGTRINYEWFHCTPIKEPQSGSVIKLWARGGPSCDKRGEYKTIVKRITRDYEPNDE
HLSFCIIENDNVPPVHYPIHEDKGEPGYVAYVGYDTDSELVQELCADSTIYHM</string>
                    <external_references type="UNIPROTKB">Q03579</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="4">
                <name>1,2-Distearoyl-sn-glycerophosphoethanolamine</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000748065</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <formula>3PE</formula>
            </ligand>
            <ligand macromolecule_id="5">
                <name>hexacosanoic acid</name>
                <molecular_weight>
                    <theoretical units="MDa">0.00039669</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>7PO</formula>
            </ligand>
            <ligand macromolecule_id="6">
                <name>[(2S)-1-hexadecanoyloxy-3-[hydroxy-[(2S,3R,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] heptadecanoate</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000825059</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>PIJ</formula>
            </ligand>
            <ligand macromolecule_id="7">
                <name>AMMONIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">1.8038e-05</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>NH4</formula>
            </ligand>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <buffer>
                        <ph>6.5</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>TFS GLACIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_defocus_min units="µm">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <specialist_optics>
                        <energy_filter>
                            <name>TFS Selectris</name>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TFS FALCON 4i (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">50.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <ctf_correction>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>159440</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="364501">
        <file>emd_18652.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>450</col>
            <row>450</row>
            <sec>450</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>450</x>
            <y>450</y>
            <z>450</z>
        </spacing>
        <cell>
            <a units="Å">306.0</a>
            <b units="Å">306.0</b>
            <c units="Å">306.0</c>
            <alpha units="deg">90.0</alpha>
            <beta units="deg">90.0</beta>
            <gamma units="deg">90.0</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-0.5720945</minimum>
            <maximum>0.958738</maximum>
            <average>0.000069158945</average>
            <std>0.018881474</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.68</x>
            <y units="Å">0.68</y>
            <z units="Å">0.68</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.16</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-18652::::</label>
    </map>
    <interpretation>
        <segmentation_list>
            <segmentation>
                <file>emd_18652_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="364501">
                <file>emd_18652_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>450</col>
                    <row>450</row>
                    <sec>450</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>450</x>
                    <y>450</y>
                    <z>450</z>
                </spacing>
                <cell>
                    <a units="Å">306.0</a>
                    <b units="Å">306.0</b>
                    <c units="Å">306.0</c>
                    <alpha units="deg">90.0</alpha>
                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
                </cell>
                <axis_order>
                    <fast>X</fast>
                    <medium>Y</medium>
                    <slow>Z</slow>
                </axis_order>
                <statistics>
                    <minimum>-0.781355</minimum>
                    <maximum>0.7527347</maximum>
                    <average>0.0004994046</average>
                    <std>0.09256151</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.68</x>
                    <y units="Å">0.68</y>
                    <z units="Å">0.68</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-18652::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="364501">
                <file>emd_18652_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>450</col>
                    <row>450</row>
                    <sec>450</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>450</x>
                    <y>450</y>
                    <z>450</z>
                </spacing>
                <cell>
                    <a units="Å">306.0</a>
                    <b units="Å">306.0</b>
                    <c units="Å">306.0</c>
                    <alpha units="deg">90.0</alpha>
                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
                </cell>
                <axis_order>
                    <fast>X</fast>
                    <medium>Y</medium>
                    <slow>Z</slow>
                </axis_order>
                <statistics>
                    <minimum>-0.786357</minimum>
                    <maximum>0.7420403</maximum>
                    <average>0.00049611216</average>
                    <std>0.09256249</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.68</x>
                    <y units="Å">0.68</y>
                    <z units="Å">0.68</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-18652::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
