<emd emdb_id="EMD-6359" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
    <admin>
        <current_status>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-06-20</deposition>
            <header_release>2015-07-15</header_release>
            <map_release>2015-07-22</map_release>
            <update>2016-05-04</update>
        </key_dates>
        <title>Cryo-EM structure of the peroxisomal Pex1/Pex6 complex in ATP-gamma-S state</title>
        <authors_list>
            <author>Blok NB</author>
            <author>Tan D</author>
            <author>Wang RY</author>
            <author>Penczek PA</author>
            <author>Baker D</author>
            <author>DiMaio F</author>
            <author>Rapoport TA</author>
            <author>Walz T</author>
        </authors_list>
        <keywords>AAA ATPase, cryoelectron microscopy, peroxisome</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Blok NB</author>
                    <author order="2">Tan D</author>
                    <author order="3">Wang RY</author>
                    <author order="4">Penczek PA</author>
                    <author order="5">Baker D</author>
                    <author order="6">DiMaio F</author>
                    <author order="7">Rapoport TA</author>
                    <author order="8">Walz T</author>
                    <title>Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>112</volume>
                    <first_page>e4017</first_page>
                    <last_page>e4025</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26170309</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1500257112</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Peroxisomal Pex1/Pex6 ATPase complex</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Peroxisomal Pex1/Pex6 ATPase complex</name>
                <details>The sample was freshly prepared before being loaded onto grids.</details>
                <oligomeric_state>heterohexamer formed by three Pex1 and three Pex6</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.726</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Pex1">Peroxisomal ATPase Pex1</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>yeast</synonym_organism>
                    <organelle>peroxisome</organelle>
                    <cellular_location>cytoplasm</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.122</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>Three molecules of Pex1 interact with three molecules of Pex6 to form a heterohexamer of alternating subunits.</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                    <recombinant_strain>InvSc1</recombinant_strain>
                    <recombinant_plasmid>pRS423 Gal1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P24004</external_references>
                    <external_references type="INTERPRO">IPR025653</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="Pex6">Peroxisomal ATPase Pex6</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <synonym_organism>yeast</synonym_organism>
                    <organelle>peroxisome</organelle>
                    <cellular_location>cytoplasm</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.120</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <oligomeric_state>Three molecules of Pex1 interact with three molecules of Pex6 to form a heterohexamer of alternating subunits.</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="4932">Saccharomyces cerevisiae</recombinant_organism>
                    <recombinant_strain>InvSc1</recombinant_strain>
                    <recombinant_plasmid>pRS424 Gal1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P33760</external_references>
                </sequence>
            </protein_or_peptide>
        </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">0.6</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>50 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1mM DTT, 0.3 mM ATP-gamma-S</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil 400 mesh holey carbon grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>FEI VITROBOT MARK I</instrument>
                        <method>Blot for 5 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">-0.9</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">-2.2</nominal_defocus_max>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <calibrated_magnification>40410.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <details>Images were recorded using a Gatan K2 Summit in super-resolution counting mode. Motion correction as described in Li et al. (2013) Nature Methods.</details>
                    <date>2014-05-13</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <number_real_images>1169</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">38</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Oxford instrument nitrogen-cooled side-entry holder</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.2</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPARX, RELION</name>
                        </software>
                    </software_list>
                    <details>Initial model building was done in SPARX using the common-line method. 3D classification, refinement, and subsequent reconstruction were performed using RELION.</details>
                    <number_images_used>46655</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_6359.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>240</col>
            <row>240</row>
            <sec>240</sec>
        </dimensions>
        <origin>
            <col>-120</col>
            <row>-120</row>
            <sec>-120</sec>
        </origin>
        <spacing>
            <x>240</x>
            <y>240</y>
            <z>240</z>
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        <cell>
            <a units="&#8491;">297.6</a>
            <b units="&#8491;">297.6</b>
            <c units="&#8491;">297.6</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>-0.00397698</minimum>
            <maximum>0.02711316</maximum>
            <average>-0.000012</average>
            <std>0.00245146</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.24</x>
            <y units="&#8491;">1.24</y>
            <z units="&#8491;">1.24</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0123</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Pex1/Pex6 AAA ATPase complex in ATP-gamma-S using single-particle cryo-electron microscopy without imposed symmetry</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6359::::</details>
    </map>
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