<?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_2/emdb.xsd" version="3.0.9.2" emdb_id="EMD-21307">
    <admin>
        <current_status>
            <date>2024-03-06</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-02-02</deposition>
            <header_release>2020-09-23</header_release>
            <map_release>2020-09-23</map_release>
            <update>2024-03-06</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 human NatB complex</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 ORCID="0000-0001-7798-4317" order="1">Deng S</author>
                    <author order="2">Pan B</author>
                    <author order="3">Gottlieb L</author>
                    <author order="4">Petersson J</author>
                    <author ORCID="0000-0003-4373-4752" order="5">Marmorstein R</author>
                    <title>Molecular basis for N-terminal alpha-synuclein acetylation by human NatB.</title>
                    <journal_abbreviation>Elife</journal_abbreviation>
                    <country>US</country>
                    <volume>9</volume>
                    <year>2020</year>
                    <external_references type="PUBMED">32885784</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.57491</external_references>
                    <external_references type="ISSN">2050-084X</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6vp9</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>human NatB complex</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>human NatB complex</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>N-alpha-acetyltransferase 20, N-alpha-acetyltransferase 25, NatB auxiliary subunit</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>MDVFM peptide</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>N-alpha-acetyltransferase 20</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.018694168</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MTTLRAFTCDDLFRFNNINLDPLTETYGIPFYLQYLAHWPEYFIVAEAPGGELMGYIMGKAEGSVAREEWHGHVTALSVA
PEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEYYSASNGEPDEDAYDMRKALSRDT
EKK</string>
                    <external_references type="UNIPROTKB">P61599</external_references>
                </sequence>
                <ec_number>2.3.1.254</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>N-alpha-acetyltransferase 25, NatB auxiliary subunit</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.11244425799999999</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MATRGHVQDPNDRRLRPIYDYLDNGNNKMAIQQADKLLKKHKDLHCAKVLKAIGLQRTGKQEEAFTLAQEVAALEPTDDN
SLQALTILYREMHRPELVTKLYEAAVKKVPNSEEYHSHLFMAYARVGEYKKMQQAGMALYKIVPKNPYYFWSVMSLIMQS
ISAQDENLSKTMFLPLAERMVEKMVKEDKIEAEAEVELYYMILERLGKYQEALDVIRGKLGEKLTSEIQSRENKCMAMYK
KLSRWPECNALSRRLLLKNSDDWQFYLTYFDSVFRLIEEAWSPPAEGEHSLEGEVHYSAEKAVKFIEDRITEESKSSRHL
RGPHLAKLELIRRLRSQGCNDEYKLGDPEELMFQYFKKFGDKPCCFTDLKVFVDLLPATQCTKFINQLLGVVPLSTPTED
KLALPADIRALQQHLCVVQLTRLLGLYHTMDKNQKLSVVRELMLRYQHGLEFGKTCLKTELQFSDYYCLLAVHALIDVWR
ETGDETTVWQALTLLEEGLTHSPSNAQFKLLLVRIYCMLGAFEPVVDLYSSLDAKHIQHDTIGYLLTRYAESLGQYAAAS
QSCNFALRFFHSNQKDTSEYIIQAYKYGAFEKIPEFIAFRNRLNNSLHFAQVRTERMLLDLLLEANISTSLAESIKSMNL
RPEEDDIPWEDLRDNRDLNVFFSWDPKDRDVSEEHKKLSLEEETLWLRIRSLTLRLISGLPSLNHPVEPKNSEKTAENGV
SSRIDILRLLLQQLEATLETGKRFIEKDIQYPFLGPVPTRMGGFFNSGCSQCQISSFYLVNDIYELDTSGLEDTMEIQER
IENSFKSLLDQLKDVFSKCKGDLLEVKDGNLKTHPTLLENLVFFVETISVILWVSSYCESVLRPYKLNLQKKKKKKKETS
IIMPPVFTSFQDYVTGLQTLISNVVDHIKGLETHLIALKLEELILEDTSLSPEERKFSKTVQGKVQSSYLHSLLEMGELL
KKRLETTKKLKI</string>
                    <external_references type="UNIPROTKB">Q14CX7</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>MDVFM peptide</name>
                <natural_source database="NCBI">
                    <organism ncbi="83333">Escherichia coli K-12</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.000641799</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MDVFM</string>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="4">
                <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>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.46</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>982420</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="42593">
        <file>emd_21307.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>220</col>
            <row>220</row>
            <sec>220</sec>
        </dimensions>
        <origin>
            <col>-110</col>
            <row>-110</row>
            <sec>-110</sec>
        </origin>
        <spacing>
            <x>220</x>
            <y>220</y>
            <z>220</z>
        </spacing>
        <cell>
            <a units="Å">182.59999</a>
            <b units="Å">182.59999</b>
            <c units="Å">182.59999</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>-0.111868426</minimum>
            <maximum>0.16999745</maximum>
            <average>0.0002937734</average>
            <std>0.005049073</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.83</x>
            <y units="Å">0.83</y>
            <z units="Å">0.83</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.015</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-21307::::</label>
        <annotation_details>NatB complex</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
