<emd emdb_id="EMD-5772" 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>2013-10-23</deposition>
            <header_release>2013-11-06</header_release>
            <map_release>2013-11-06</map_release>
            <update>2013-12-04</update>
        </key_dates>
        <title>A Two-Pronged Structural Analysis of Retroviral Maturation Indicates that Core Formation Proceeds by a Disassembly-Reassembly Pathway Rather than a Displacive Transition</title>
        <authors_list>
            <author>Keller PW</author>
            <author>Huang RK</author>
            <author>England M</author>
            <author>Waki K</author>
            <author>Cheng N</author>
            <author>Heymann JB</author>
            <author>Craven RC</author>
            <author>Freed EO</author>
            <author>Steven AC</author>
        </authors_list>
        <keywords>Cryo-EM, Rous Sarcoma Virus Structure, in vitro assembled capsids, spacer peptide</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Keller PW</author>
                    <author order="2">Huang R</author>
                    <author order="3">England M</author>
                    <author order="4">Waki K</author>
                    <author order="5">Cheng N</author>
                    <author order="6">Heymann JB</author>
                    <author order="7">Craven RC</author>
                    <author order="8">Freed EO</author>
                    <author order="9">Steven AC</author>
                    <title>A two-pronged structural analysis of retroviral maturation indicates that core formation proceeds by a disassembly-reassembly pathway, rather than a displacive transition.</title>
                    <journal>J.VIROL.</journal>
                    <volume>87</volume>
                    <first_page>13655</first_page>
                    <last_page>13664</last_page>
                    <year>2013</year>
                    <external_references type="PUBMED">24109217</external_references>
                    <external_references type="DOI">doi:10.1128/JVI.01408-13</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>T=1 icosahedral assembly of Rous sarcoma virus capsid proteins with spacer peptide</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>T=1 icosahedral assembly of Rous sarcoma virus capsid proteins with spacer peptide</name>
                <oligomeric_state>T=1 icosahedral shell with 60 subunits forming 12 pentamers</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">1.51</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Rous sarcoma virus</name>
                <details>icosahedral assembly of CA-SP protein</details>
                <sci_species_name ncbi="11886">Rous sarcoma virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9031">Gallus gallus</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21</recombinant_strain>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">1.51</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <triangulation>1</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>true</virus_empty>
            </virus_supramolecule>
        </supramolecule_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">2</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>10 mM Tris-HCl, 75 mM sodium chloride, 0.05 mM EDTA, 0.5 M sodium phosphate</details>
                    </buffer>
                    <grid>
                        <details>Holey carbon film on R2/2 400 mesh copper grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">93.15</chamber_temperature>
                        <instrument>LEICA KF80</instrument>
                        <details>Vitrification carried out in nitrogen atmosphere.</details>
                        <method>4.0 microliter sample dropped onto grid, blotted on one side for 2 second, then plunged.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM200FEG</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.7</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">93.15</temperature_average>
                    </temperature>
                    <date>2011-09-24</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">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>17</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were selected manually and processed with Bsoft.</details>
                <ctf_correction>
                    <details>CTF was determined from the whole micrograph. Phase reversal and baseline correction were applied to each extracted particle.</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.5</resolution>
                    <resolution_method>FSC 0.33 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                        </software>
                    </software_list>
                    <number_images_used>2663</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="61037">
        <file>emd_5772.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>250</col>
            <row>250</row>
            <sec>250</sec>
        </dimensions>
        <origin>
            <col>-125</col>
            <row>-125</row>
            <sec>-125</sec>
        </origin>
        <spacing>
            <x>250</x>
            <y>250</y>
            <z>250</z>
        </spacing>
        <cell>
            <a units="&#8491;">317.5</a>
            <b units="&#8491;">317.5</b>
            <c units="&#8491;">317.5</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>-2.68567443</minimum>
            <maximum>6.42209005</maximum>
            <average>0.0</average>
            <std>0.82537431</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.27</x>
            <y units="&#8491;">1.27</y>
            <z units="&#8491;">1.27</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>T=1 icosahedral assembly of Rous sarcoma virus CA-SP protein</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5772::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1EM9</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>RSV CA NTD and CTD structures were rigid-body fitted into the T=1 density map using Chimera fit to map tools.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>1EOQ</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>RSV CA NTD and CTD structures were rigid-body fitted into the T=1 density map using Chimera fit to map tools.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_5772.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
    <validation>
        <fsc_curve>
            <file>emd_5772_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>