<?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_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-23110">
    <admin>
        <current_status>
            <date>2024-05-29</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-12-14</deposition>
            <header_release>2021-05-12</header_release>
            <map_release>2021-05-12</map_release>
            <update>2024-05-29</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R35 GM118090</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of S. Pombe NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate</title>
        <authors_list>
            <author>Deng S</author>
            <author>Marmorstein R</author>
        </authors_list>
        <keywords>NatB, NAA20, NAA25, TRANSFERASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Deng S</author>
                    <author order="2">Gottlieb L</author>
                    <author order="3">Pan B</author>
                    <author order="4">Supplee J</author>
                    <author order="5">Wei X</author>
                    <author order="6">Petersson EJ</author>
                    <author order="7">Marmorstein R</author>
                    <title>Molecular mechanism of N-terminal acetylation by the ternary NatC complex.</title>
                    <journal_abbreviation>Structure</journal_abbreviation>
                    <country>UK</country>
                    <volume>29</volume>
                    <first_page>1094</first_page>
                    <year>2021</year>
                    <external_references type="PUBMED">34019809</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2021.05.003</external_references>
                    <external_references type="ISSN">0969-2126</external_references>
                    <external_references type="CSD">2005</external_references>
                    <external_references type="ASTM">STRUE6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>7l1k</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>heterotimeric S.pombe NatC complex with a bisubstrate inhibitor and inositol hexaphosphate</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>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>N-alpha-acetyltransferase NatC, catalytic subunit NAA30,
auxiliary subunits NAA35 and NAA38</name>
                <parent>1</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="4896">Schizosaccharomyces pombe</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>CoA-Ac-MLGP bi-substrate</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>N-alpha-acetyltransferase 30</name>
                <natural_source database="NCBI">
                    <organism ncbi="284812">Schizosaccharomyces pombe (strain 972 / ATCC 24843)</organism>
                    <strain>972 / ATCC 24843</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.017721349999999997</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MVTIVPYSHQYLKDICQLIQKDLSEPYSKYVYRYFVHQWPEFSFVALDNDRFIGAVICKQDVHRGTTLRGYIAMLAIVKE
YRGQGIATKLTQASLDVMKNRGAQEIVLETEVDNEAAMSFYERLGFCRYKRLYRYYLNGTDAFRYILYPN</string>
                    <external_references type="UNIPROTKB">O74311</external_references>
                </sequence>
                <ec_number>2.3.1.256</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>N-alpha-acetyltransferase 35, NatC auxiliary subunit</name>
                <natural_source database="NCBI">
                    <organism ncbi="284812">Schizosaccharomyces pombe (strain 972 / ATCC 24843)</organism>
                    <strain>972 / ATCC 24843</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.080541312</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MSVKESLSLLNSMQGNVKIGNVEPAKGNEGYVDNAGYVDCTKSYFEATKSLKEEQLVCDPKFTLLDSISAFEIMEPKMDS
GIDYQPLRVDFSRDLSYLEILALMDLIVSAEKEWHYGSPLSESLLCSAHVFSICKSPISQVGDSGFSSGSGRNTTDIVLF
PFVLAVIKCCDIVHREFLMGNLYDEEDISSFSYHMSFLQNYPIEKLNYLLQSSIEYLASEVIKFSAELRQIIEGILNRIQ
LRIGILRVYERSDIKTTIDALHLIKNLVPEIQNTVSVVDSSIKESILKQYWDFRVQAQLVATAPVRNIPPTGIEHSYQRI
LYFADDMLLILNSHTLASSLAVYQFCLDFTRLNRTPEPYVRSSLQALITANNAVNLRDQPTSYMLECIREFSGLPSNFYN
PNTRTVIEKNSISSAYGPLVESLIAHSTNIMVDLVRICSHNPCRFRRNLINLLPEITVAHFEAEALDLKFVAKSLPSNGP
FSSFIYHVKLNAIEHILLSSFEQKLHQPYQWPHFFAVLDHVFSIHQTHLELHGKDRNTPPMAKTFVTYLHRILNAIKETY
SGYLLLTVLCMRLNIIKTPSFTLDEKIQESYYMAHYRPLINLRQPKPLLRSEADCIIKNLQNFSTDDLIIKSNEKFTAAK
NSLINVIKSGFEQNEFINPYFLQTNYLKNLLCCCITNLVSLAILSKDHSANLKIVEIPGNPLPSLSRT</string>
                    <external_references type="UNIPROTKB">Q9USY3</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>N-alpha-acetyltransferase 38, NatC auxiliary subunit</name>
                <natural_source database="NCBI">
                    <organism ncbi="284812">Schizosaccharomyces pombe (strain 972 / ATCC 24843)</organism>
                    <strain>972 / ATCC 24843</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.013258555</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MALHYFLQYDVQILCIALMFSIFRVCISTAIDFTSPKLDEFSLIMEMGEILLTSWLNRSVHIEIFDERKFIGKFLCTDRE
GAAILSNTTEYNKGFSRALGLVVIPGKHIKSFSVRA</string>
                    <external_references type="UNIPROTKB">O43080</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name>MLGP peptide</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.000416535</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MLGP</string>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="5">
                <name>INOSITOL HEXAKISPHOSPHATE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.0006600349999999999</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>IHP</formula>
            </ligand>
            <ligand macromolecule_id="6">
                <name>CARBOXYMETHYL COENZYME *A</name>
                <molecular_weight>
                    <theoretical units="MDa">0.00082557</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <formula>CMC</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">
                    <concentration units="mg/mL">1.0</concentration>
                    <buffer>
                        <ph>7.0</ph>
                        <component>
                            <concentration units="mM">200.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium cloride</name>
                        </component>
                        <component>
                            <concentration units="mM">25.0</concentration>
                            <formula>Hepes</formula>
                            <name>4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>DTT</formula>
                            <name>Dithiothreitol</name>
                        </component>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">289</chamber_temperature>
                        <instrument>FEI VITROBOT MARK II</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">1.6</average_electron_dose_per_image>
                        </image_recording>
                        <image_recording image_recording_id="2">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">1.3</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>
                <details>5397 images</details>
                <particle_selection>
                    <number_selected>3289528</number_selected>
                </particle_selection>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <resolution units="Å" res_type="BY AUTHOR">3.16</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>v2</version>
                        </software>
                    </software_list>
                    <number_images_used>607131</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>v2</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>v2</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <number_classes>4</number_classes>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                            <version>v2</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32001">
        <file>emd_23110.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-100</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="Å">168.0</a>
            <b units="Å">168.0</b>
            <c units="Å">168.0</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>-1.4852304</minimum>
            <maximum>2.416325</maximum>
            <average>0.0013826761</average>
            <std>0.11161481</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.84</x>
            <y units="Å">0.84</y>
            <z units="Å">0.84</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.252</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-23110::::</label>
        <annotation_details>NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <segmentation_list>
            <segmentation>
                <file>emd_23110_msk_1.map</file>
            </segmentation>
        </segmentation_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="32001">
                <file>emd_23110_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>200</col>
                    <row>200</row>
                    <sec>200</sec>
                </dimensions>
                <origin>
                    <col>-100</col>
                    <row>-100</row>
                    <sec>-100</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>200</z>
                </spacing>
                <cell>
                    <a units="Å">168.0</a>
                    <b units="Å">168.0</b>
                    <c units="Å">168.0</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>-0.1865801</minimum>
                    <maximum>0.7362586</maximum>
                    <average>0.0014721793</average>
                    <std>0.05456115</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.84</x>
                    <y units="Å">0.84</y>
                    <z units="Å">0.84</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-23110::::</label>
                <annotation_details>NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="32001">
                <file>emd_23110_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>200</col>
                    <row>200</row>
                    <sec>200</sec>
                </dimensions>
                <origin>
                    <col>-100</col>
                    <row>-100</row>
                    <sec>-100</sec>
                </origin>
                <spacing>
                    <x>200</x>
                    <y>200</y>
                    <z>200</z>
                </spacing>
                <cell>
                    <a units="Å">168.0</a>
                    <b units="Å">168.0</b>
                    <c units="Å">168.0</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>-0.18058333</minimum>
                    <maximum>0.7336943</maximum>
                    <average>0.0014376085</average>
                    <std>0.054563586</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">0.84</x>
                    <y units="Å">0.84</y>
                    <z units="Å">0.84</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-23110::::</label>
                <annotation_details>NatC complex with a Bisubstrate inhibitor and inositol hexaphosphate</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
