<emd emdb_id="EMD-6592" 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>2016-02-11</deposition>
            <header_release>2016-04-27</header_release>
            <map_release>2016-07-13</map_release>
            <update>2016-07-20</update>
        </key_dates>
        <title>CSF_closed_trimer in complex with the bnAb PGV04</title>
        <authors_list>
            <author>Kong P</author>
            <author>He L</author>
            <author>de Val N</author>
            <author>Morris CD</author>
            <author>Vora N</author>
            <author>Azadnia P</author>
            <author>Sok D</author>
            <author>Zhou B</author>
            <author>Burton DR</author>
            <author>Ward AB</author>
            <author>Wilson IA</author>
            <author>Zhu J</author>
        </authors_list>
        <keywords>HIV, envelope, glycoprotein, trimer</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Kong L</author>
                    <author order="2">He L</author>
                    <author order="3">de Val N</author>
                    <author order="4">Vora N</author>
                    <author order="5">Morris CD</author>
                    <author order="6">Azadnia P</author>
                    <author order="7">Sok D</author>
                    <author order="8">Zhou B</author>
                    <author order="9">Burton DR</author>
                    <author order="10">Ward AB</author>
                    <author order="11">Wilson IA</author>
                    <author order="12">Zhu J</author>
                    <title>Uncleaved prefusion-optimized gp140 trimers derived from analysis of HIV-1 envelope metastability.</title>
                    <journal>Nature Communications</journal>
                    <volume>7</volume>
                    <first_page>12040</first_page>
                    <last_page>12040</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27349805</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms12040</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>CSF trimer closed, bound to PGV04</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>CSF trimer closed, bound to PGV04</name>
                <oligomeric_state>one trimer bound to three Fabs</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.570</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>CSF</name>
                <natural_source database="NCBI">
                    <organism ncbi="12721">Human immunodeficiency virus</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.570</experimental>
                    <theoretical units="MDa">0.570</theoretical>
                </molecular_weight>
                <details>Heterodimer of gp120 and gp41 assembles into a trimer.</details>
                <number_of_copies>2</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>HEK 293F</recombinant_cell>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="Fab">PGV04</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                    <recombinant_cell>HEK 293F</recombinant_cell>
                </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">0.02</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM Tris-HCl, 150 mM NaCl</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Grids were glow-discharged at 20 mA for 30 seconds and stained with 2% uranyl formate for 40 seconds.</details>
                    </staining>
                    <grid>
                        <details>400 Cu mesh grids</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">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.0</nominal_defocus_max>
                    <nominal_magnification>46000.0</nominal_magnification>
                    <calibrated_magnification>52000.0</calibrated_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2015-08-20</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>119</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">30.15</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;">21.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2, sparx</name>
                        </software>
                    </software_list>
                    <number_images_used>10706</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>104</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="2001">
        <file>emd_6592.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>80</col>
            <row>80</row>
            <sec>80</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>80</x>
            <y>80</y>
            <z>80</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>-48.714134219999998</minimum>
            <maximum>114.063644409999995</maximum>
            <average>1.15237343</average>
            <std>8.868695260000001</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.1</x>
            <y units="&#8491;">4.1</y>
            <z units="&#8491;">4.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>30.600000000000001</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of CSF closed conformation trimer bound to PGV04</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6592::::</details>
    </map>
</emd>