<emd emdb_id="EMD-5275" 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>2011-04-15</deposition>
            <header_release>2011-04-19</header_release>
            <map_release>2011-08-16</map_release>
            <update>2011-08-16</update>
        </key_dates>
        <title>4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus</title>
        <authors_list>
            <author>Zhang R</author>
            <author>Hryc CF</author>
            <author>Cong Y</author>
            <author>Liu X</author>
            <author>Jakana J</author>
            <author>Gorchakov R</author>
            <author>Baker ML</author>
            <author>Weaver SC</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>alphavirus, bioweapon, cryoEM, modeling, VEEV</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang R</author>
                    <author order="2">Hryc CF</author>
                    <author order="3">Cong Y</author>
                    <author order="4">Liu X</author>
                    <author order="5">Jakana J</author>
                    <author order="6">Gorchakov R</author>
                    <author order="7">Baker ML</author>
                    <author order="8">Weaver SC</author>
                    <author order="9">Chiu W</author>
                    <title>4.4 Angstrom Cryo-EM Structure of an Enveloped Alphavirus Venezuelan Equine Encephalitis Virus</title>
                    <journal>EMBO J.</journal>
                    <volume>30</volume>
                    <first_page>3854</first_page>
                    <last_page>3863</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">21829169</external_references>
                    <external_references type="DOI">doi:10.1038/emboj.2011.261</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j0c</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
            <pdb_reference>
                <pdb_id>3j0g</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Venezuelan Equine Encephalitis Virus, TC-83 Strain</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Venezuelan Equine Encephalitis Virus, TC-83 Strain</name>
                <details>The viruses were purified from infected Baby hamster kidney (BHK) cells</details>
                <oligomeric_state>E1-E2-E3-CP complex</oligomeric_state>
                <number_unique_components>4</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">52</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="VEEV">Venezuelan equine encephalitis virus</name>
                <details>The VEEV virus has 240 copies of E1, E2, and CP arranged in icosahedral symmetry</details>
                <sci_species_name ncbi="11036">Venezuelan equine encephalitis virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9796">Equus caballus</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <molecular_weight>
                    <theoretical units="MDa">52</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <diameter units="&#8491;">700</diameter>
                    <triangulation>4</triangulation>
                </virus_shell>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>true</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>VEEV</syn_species_name>
            </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">
                    <buffer>
                        <ph>7.0</ph>
                    </buffer>
                    <grid>
                        <details>400 mesh Quantifoil R 1.2/1.3 copper grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: Vitrobot</details>
                        <method>2 blots, each blot 2 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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_cs units="mm">3.2</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.4</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>100000.0</nominal_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">96</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism was corrected at 100,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>Omega Filter</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2008-04-09</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                            <detector_distance>200</detector_distance>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Eucentric</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each frame</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.8</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <number_images_used>37000</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>1000</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="65537">
        <file>emd_5275.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>-108</col>
            <row>-18</row>
            <sec>-348</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="&#8491;">273.92</a>
            <b units="&#8491;">273.92</b>
            <c units="&#8491;">273.92</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-4.94263</minimum>
            <maximum>10.6478</maximum>
            <average>-0.000000008421</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.07</x>
            <y units="&#8491;">1.07</y>
            <z units="&#8491;">1.07</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a portion of the original 3D density map (size 800x800x800 pixels) of Venezuelan Equine Encephalitis Virus TC-83 strain.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5275::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3N40</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <details>Protocol: Rigid Body</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>