<emd emdb_id="EMD-6542" 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>2015-11-24</deposition>
            <header_release>2016-04-27</header_release>
            <map_release>2017-05-24</map_release>
            <update>2017-08-02</update>
        </key_dates>
        <title>Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5</title>
        <authors_list>
            <author>Hu G</author>
            <author>Liu J</author>
            <author>Roux KH</author>
            <author>Taylor KA</author>
        </authors_list>
        <keywords>Cryoelectron tomography, image processing, electron microscopy, immunology, AIDS, HIV</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hu G</author>
                    <author order="2">Liu J</author>
                    <author order="3">Roux KH</author>
                    <author order="4">Taylor KA</author>
                    <title>Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5.</title>
                    <journal>J.VIROL.</journal>
                    <year>2017</year>
                    <external_references type="PUBMED">28539445</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.00134-17</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3jcb</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>SIV envelope bound to CD4 and monoclonal antibody 36D5 in closed state</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>SIV envelope bound to CD4 and monoclonal antibody 36D5 in closed state</name>
                <oligomeric_state>gp120 trimer bound to CD4 and one antibody 36D5</oligomeric_state>
                <number_unique_components>3</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="SIV">Simian immunodeficiency virus</name>
                <sci_species_name ncbi="11723">Simian immunodeficiency virus</sci_species_name>
                <sci_species_strain>SIV239/251tail/Supt-CCR5 CL.30</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="9527">Cercopithecidae</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>SIV</syn_species_name>
            </virus_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="CD4">T-cell surface glycoprotein CD4</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>human</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>monoclonal antibody 36D5</name>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <synonym_organism>mouse</synonym_organism>
                </natural_source>
                <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>subtomogramAveraging</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <instrument>HOMEMADE PLUNGER</instrument>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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>
                    <nominal_defocus_min units="&#181;m">4.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">5.0</nominal_defocus_max>
                    <nominal_magnification>31000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <date>2008-08-16</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F415 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>cryo holder</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-65</min_angle>
                            <max_angle units="deg">65</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <final_reconstruction>
                    <software_list>
                        <software>
                            <name>I3, protomo</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>1181</number_subtomograms_used>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="357">
        <file>emd_6542.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>45</col>
            <row>45</row>
            <sec>45</sec>
        </dimensions>
        <origin>
            <col>-22</col>
            <row>-22</row>
            <sec>-22</sec>
        </origin>
        <spacing>
            <x>45</x>
            <y>45</y>
            <z>45</z>
        </spacing>
        <cell>
            <a units="&#8491;">256.5</a>
            <b units="&#8491;">256.5</b>
            <c units="&#8491;">256.5</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>-0.53380328</minimum>
            <maximum>2.71820331</maximum>
            <average>0.50926995</average>
            <std>0.61779344</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">5.7</x>
            <y units="&#8491;">5.7</y>
            <z units="&#8491;">5.7</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.6</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of closed state SIV envelope spike bound with CD4 and 36D5</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6542::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4NCO</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_6542.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>