<emd emdb_id="EMD-3076" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-07-05</deposition>
            <header_release>2015-07-29</header_release>
            <map_release>2016-03-16</map_release>
            <update>2016-04-06</update>
        </key_dates>
        <title>Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site</title>
        <authors_list>
            <author>Liu C</author>
            <author>Perilla JR</author>
            <author>Ning J</author>
            <author>Lu M</author>
            <author>Hou G</author>
            <author>Ramalhu R</author>
            <author>Bedwell GJ</author>
            <author>Ahn J</author>
            <author>Shi J</author>
            <author>Gronenborn AM</author>
            <author>Prevelige Jr PE</author>
            <author>Rousso I</author>
            <author>Aiken C</author>
            <author>Polenova T</author>
            <author>Schulten K</author>
            <author>Zhang P</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Liu C</author>
                    <author order="2">Perilla JR</author>
                    <author order="3">Ning J</author>
                    <author order="4">Lu M</author>
                    <author order="5">Hou G</author>
                    <author order="6">Ramalhu R</author>
                    <author order="7">Bedwell GJ</author>
                    <author order="8">Ahn J</author>
                    <author order="9">Shi J</author>
                    <author order="10">Gronenborn AM</author>
                    <author order="11">Prevelige Jr PE</author>
                    <author order="12">Rousso I</author>
                    <author order="13">Aiken C</author>
                    <author order="14">Polenova T</author>
                    <author order="15">Schulten K</author>
                    <author order="16">Zhang P</author>
                    <title>Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non-canonical Binding Site</title>
                    <journal>NAT.COMMUN.</journal>
                    <volume>7</volume>
                    <first_page>10714</first_page>
                    <last_page>10714</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26940118</external_references>
                    <external_references type="DOI">doi:10.1038/NCOMMS10714</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5fjb</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Helical assembly of HIV-1 capsid protein and host cell factor Cyclophilin A</name>
                <oligomeric_state>hexamer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.042</experimental>
                    <theoretical units="MDa">0.042</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="HIV-1 capsid protein with CypA">Human immunodeficiency virus 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="11676">Human immunodeficiency virus 1</organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.042</experimental>
                    <theoretical units="MDa">0.042</theoretical>
                </molecular_weight>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>helicalArray</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">2</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>1m NaCl,50mM Tris-Hcl</details>
                    </buffer>
                    <grid>
                        <details>Glow discharged perforated Quantifoil R2/1 grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">120</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl,50mM Tris,PH 8.0)to back side. Blot 3-5 seconds from back side.</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_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">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>59000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2013-06-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.349</sampling_interval>
                            </digitization_details>
                            <number_real_images>19</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <bits_per_pixel>32.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>side entry</specimen_holder>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>The particles were aligned using IHRSR</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">7.393</delta_z>
                            <delta_phi units="deg">138.133</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER, IHRSR</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="193068">
        <file>emd_3076.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>436</col>
            <row>436</row>
            <sec>260</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>436</x>
            <y>436</y>
            <z>260</z>
        </spacing>
        <cell>
            <a units="&#8491;">462.15997</a>
            <b units="&#8491;">462.15997</b>
            <c units="&#8491;">275.59998</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>-44.915374759999999</minimum>
            <maximum>57.380767820000003</maximum>
            <average>0.24355465</average>
            <std>11.38533211</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.06</x>
            <y units="&#8491;">1.06</y>
            <z units="&#8491;">1.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>20.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction by aligning both CA and Cypa</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3076::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3J4F</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>
                <initial_model>
                    <access_code>1AK4</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>