<emd emdb_id="EMD-6335" 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>2015-05-06</deposition>
            <header_release>2015-05-27</header_release>
            <map_release>2016-05-11</map_release>
            <update>2016-05-25</update>
        </key_dates>
        <title>Three-Dimensional Reconstruction of Lipid Nanodisc Reconstituted Yeast V-ATPase Membrane Sector</title>
        <authors_list>
            <author>Stam NJ</author>
            <author>Wilkens S</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Stam NJ</author>
                    <author order="2">Wilkens S</author>
                    <title>Three-Dimensional Reconstruction of Lipid Nanodisc Reconstituted Yeast V-ATPase Membrane Sector</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>V-ATPase membrane sector (Vo) isolated from yeast membranes and reconstituted with lipid nanodisc</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>V-ATPase membrane sector (Vo) isolated from yeast membranes and reconstituted with lipid nanodisc</name>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.4</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Vacuolar-type (V-) ATPase membrane sector (Vo)</name>
                <natural_source database="NCBI">
                    <organism ncbi="4932">Saccharomyces cerevisiae</organism>
                    <strain>BY4743</strain>
                    <synonym_organism>Yeast</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.3</theoretical>
                </molecular_weight>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="membrane scaffold protein, nanodisc">MSP1E3D1</name>
                <natural_source database="NCBI">
                    <organism ncbi="32630">synthetic construct</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.03</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <oligomeric_state>Dimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                    <recombinant_strain>BL21(DE3)</recombinant_strain>
                    <recombinant_plasmid>pET28a</recombinant_plasmid>
                </recombinant_expression>
                <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">0.04</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>20 mM Tris-HCl, 100 mM NaCl, 0.5 mM EDTA</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>2% w/v uranyl formate applied to grids with adsorbed protein</details>
                    </staining>
                    <grid>
                        <details>200 mesh copper grid with thin carbon support, glow-discharged in air</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2100</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.125</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.08</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <calibrated_magnification>85800.0</calibrated_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 100,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2014-11-13</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F415 (4k x 4k)</film_or_detector_model>
                            <number_real_images>390</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">17</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were selected using a monitored semi-automated selection program.</details>
                <ctf_correction>
                    <details>By micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">16.3</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2, Relion</name>
                        </software>
                    </software_list>
                    <number_images_used>47422</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3457">
        <file>emd_6335.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>96</col>
            <row>96</row>
            <sec>96</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>96</x>
            <y>96</y>
            <z>96</z>
        </spacing>
        <cell>
            <a units="&#8491;">336.0</a>
            <b units="&#8491;">336.0</b>
            <c units="&#8491;">336.0</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>-0.18370923</minimum>
            <maximum>0.34209979</maximum>
            <average>0.00211898</average>
            <std>0.02535874</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.5</x>
            <y units="&#8491;">3.5</y>
            <z units="&#8491;">3.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.035</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Lipid Nanodisc Reconstituted Yeast V-ATPase Membrane Sector</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6335::::</details>
    </map>
    <validation>
        <fsc_curve>
            <file>emd_6335_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>