<emd emdb_id="EMD-5173" 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>2010-03-09</deposition>
            <header_release>2010-08-09</header_release>
            <map_release>2010-08-09</map_release>
            <update>2011-10-11</update>
        </key_dates>
        <title>Cryo-EM structure of virion-sized hepatitis E virus-like particle</title>
        <authors_list>
            <author>Xing L</author>
            <author>Mayazaki N</author>
            <author>Li TC</author>
            <author>Simons MN</author>
            <author>Wall JS</author>
            <author>Moore M</author>
            <author>Wang CY</author>
            <author>Takeda N</author>
            <author>Wakita T</author>
            <author>Miyamura T</author>
            <author>Cheng RH</author>
        </authors_list>
        <keywords>assembly pathway</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Xing L</author>
                    <author order="2">Li TC</author>
                    <author order="3">Mayazaki N</author>
                    <author order="4">Simon MN</author>
                    <author order="5">Wall JS</author>
                    <author order="6">Moore M</author>
                    <author order="7">Wang CY</author>
                    <author order="8">Takeda N</author>
                    <author order="9">Wakita T</author>
                    <author order="10">Miyamura T</author>
                    <author order="11">Cheng RH</author>
                    <title>Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway.</title>
                    <journal>J.BIOL.CHEM.</journal>
                    <volume>285</volume>
                    <first_page>33175</first_page>
                    <last_page>33183</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20720013</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M110.106336</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3iyo</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Hepatitis E virus like particle</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Hepatitis E virus like particle</name>
                <oligomeric_state>1</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">11.8</experimental>
                    <theoretical units="MDa">12.2</theoretical>
                    <method>STEM</method>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="recombinant virus-like particle">Hepatitis E virus</name>
                <sci_species_name ncbi="12461">Hepatitis E virus</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <molecular_weight>
                    <experimental units="MDa">11.8</experimental>
                    <theoretical units="MDa">12.2</theoretical>
                </molecular_weight>
                <virus_shell shell_id="1">
                    <name>ORF2 protein</name>
                    <diameter units="&#8491;">410</diameter>
                    <triangulation>3</triangulation>
                </virus_shell>
                <virus_type>VIRUS-LIKE PARTICLE</virus_type>
                <virus_isolate>SEROTYPE</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
                <syn_species_name>recombinant virus-like particle</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">
                    <concentration units="mg/mL">1</concentration>
                    <buffer>
                        <ph>6.2</ph>
                        <details>20mM MES-K</details>
                    </buffer>
                    <grid>
                        <details>300 mesh holey carbon</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_temperature units="K">93</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: manual plunger</details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2100F</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_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <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">10</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>single-tilt</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">10.5</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>P3DR</name>
                        </software>
                    </software_list>
                    <number_images_used>4348</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="124435">
        <file>emd_5173.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>317</col>
            <row>317</row>
            <sec>317</sec>
        </dimensions>
        <origin>
            <col>-159</col>
            <row>-159</row>
            <sec>-159</sec>
        </origin>
        <spacing>
            <x>317</x>
            <y>317</y>
            <z>317</z>
        </spacing>
        <cell>
            <a units="&#8491;">634</a>
            <b units="&#8491;">634</b>
            <c units="&#8491;">634</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>-22.952999999999999</minimum>
            <maximum>30.429300000000001</maximum>
            <average>-0.0644812</average>
            <std>3.54616</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2</x>
            <y units="&#8491;">2</y>
            <z units="&#8491;">2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>5.2</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a map for the virion-sized hepatitis E virus-like particle</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5173::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2ZZQ</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Situs</name>
                    </software>
                </software_list>
                <details>PDBEntryID_givenInChain. Protocol: Rigid Body. Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs</details>
                <target_criteria>cross-correlation</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>