<emd emdb_id="EMD-6256" 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>2015-01-23</deposition>
            <header_release>2015-02-04</header_release>
            <map_release>2015-02-04</map_release>
            <update>2015-05-27</update>
        </key_dates>
        <title>A native-like SOSIP.664 trimer based on a HIV-1 subtype B env gene</title>
        <authors_list>
            <author>Pugach P</author>
            <author>Ozorowski G</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Pugach P</author>
                    <author order="2">Ozorowski G</author>
                    <author order="3">Cupo A</author>
                    <author order="4">Ringe R</author>
                    <author order="5">Yasmeen A</author>
                    <author order="6">de Val N</author>
                    <author order="7">Derking R</author>
                    <author order="8">Kim HJ</author>
                    <author order="9">Korzun J</author>
                    <author order="10">Golabek M</author>
                    <author order="11">de Los Reyes K</author>
                    <author order="12">Ketas TJ</author>
                    <author order="13">Julien JP</author>
                    <author order="14">Burton DR</author>
                    <author order="15">Wilson IA</author>
                    <author order="16">Sanders RW</author>
                    <author order="17">Klasse PJ</author>
                    <author order="18">Ward AB</author>
                    <author order="19">Moore JP</author>
                    <title>A native-like SOSIP.664 trimer based on a HIV-1 subtype B env gene</title>
                    <journal>J.VIROL.</journal>
                    <volume>89</volume>
                    <first_page>3380</first_page>
                    <last_page>3395</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">25589637</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.03473-14</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>B41 SOSIP liganded with VRC01</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>B41 SOSIP liganded with VRC01</name>
                <oligomeric_state>one B41 trimer bound to three Fabs</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.570</experimental>
                    <theoretical units="MDa">0.570</theoretical>
                    <method>Size Exclusion Chromatography (SEC)</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>B41 SOSIP.664 gp140</name>
                <natural_source database="NCBI">
                    <organism ncbi="57667">Simian-Human immunodeficiency virus</organism>
                    <synonym_organism>HIV</synonym_organism>
                </natural_source>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>trimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_cell>HEK293T</recombinant_cell>
                    <recombinant_plasmid>pPPI4</recombinant_plasmid>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>antibody VRC01 Fab</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                </natural_source>
                <number_of_copies>3</number_of_copies>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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">0.01</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM Tris-HCl, 150 mM NaCl</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>2% w/v uranyl formate for 60 seconds</details>
                    </staining>
                    <grid>
                        <details>carbon-coated 400 Cu mesh grid, glow-discharged at 20 mA for 30 seconds</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>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">0.9</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.3</nominal_defocus_max>
                    <nominal_magnification>46000.0</nominal_magnification>
                    <calibrated_magnification>52000.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <date>2014-07-07</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F416 (4k x 4k)</film_or_detector_model>
                            <number_real_images>167</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">23.12</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>50</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">17.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Sparx, EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>32943</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_6256.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>-39</col>
            <row>-39</row>
            <sec>-39</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">328.0</a>
            <b units="&#8491;">328.0</b>
            <c units="&#8491;">328.0</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>-2.01872325</minimum>
            <maximum>11.828563689999999</maximum>
            <average>-0.00000001</average>
            <std>0.93446207</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.05</x>
            <y units="&#8491;">2.05</y>
            <z units="&#8491;">2.05</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.47</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>B41 SOSIP with VRC01</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6256::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3J5M</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>