<?xml version="1.0" encoding="UTF-8"?>
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    <admin>
        <current_status>
            <date>2024-03-27</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-11-28</deposition>
            <header_release>2020-02-26</header_release>
            <map_release>2020-02-26</map_release>
            <update>2024-03-27</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Japan Agency for Medical Research and Development (AMED)</funding_body>
                <code>JP18fk0108034h0602</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Japan Agency for Medical Research and Development (AMED)</funding_body>
                <code>JP18am0101072j0001</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Ministry of Education, Culture, Sports, Science and Technology (Japan)</funding_body>
                <code>JP26102545</code>
                <country>Japan</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Ministry of Education, Culture, Sports, Science and Technology (Japan)</funding_body>
                <code>JP16H00786</code>
                <country>Japan</country>
            </grant_reference>
        </grant_support>
        <title>Cryo-EM structure of Murine Norovirus S7 VLP</title>
        <authors_list>
            <author>Song C</author>
            <author>Miyazaki N</author>
            <author>Iwasaki K</author>
            <author>Katayama K</author>
            <author>Murata K</author>
            <author>Yokoyama M</author>
            <author>Miyazaki N</author>
            <author>Iwasaki K</author>
            <author>Murakami K</author>
            <author>Katayama K</author>
            <author>Murata K</author>
        </authors_list>
        <keywords>VLP, mature, stable, VIRUS</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0001-8628-4267" order="1">Song C</author>
                    <author order="2">Takai-Todaka R</author>
                    <author order="3">Miki M</author>
                    <author order="4">Haga K</author>
                    <author order="5">Fujimoto A</author>
                    <author order="6">Ishiyama R</author>
                    <author ORCID="0000-0002-0906-6060" order="7">Oikawa K</author>
                    <author ORCID="0000-0003-1641-0365" order="8">Yokoyama M</author>
                    <author ORCID="0000-0002-4880-7300" order="9">Miyazaki N</author>
                    <author order="10">Iwasaki K</author>
                    <author order="11">Murakami K</author>
                    <author ORCID="0000-0002-7692-1151" order="12">Katayama K</author>
                    <author ORCID="0000-0001-9446-3652" order="13">Murata K</author>
                    <title>Dynamic rotation of the protruding domain enhances the infectivity of norovirus.</title>
                    <journal_abbreviation>Plos Pathog.</journal_abbreviation>
                    <country>US</country>
                    <volume>16</volume>
                    <first_page>e1008619</first_page>
                    <last_page>e1008619</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32614892</external_references>
                    <external_references type="DOI">doi:10.1371/journal.ppat.1008619</external_references>
                    <external_references type="ISSN">1553-7374</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-9735</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Murine Norovirus S7 virion with the resting P-domain conformation</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9736</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Murine Norovirus S7 virion with the rising P-domain conformation</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9737</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Murine Norovirus 1 virion with the resting P-domain conformation</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9738</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Murine Norovirus 1 virion with the rising P-domain conformation</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9739</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Human Norovirus GII.3 VLP with the resting P-domain conformation</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-9740</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>Human Norovirus GII.3 VLP with the rising P-domain conformation</details>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6iuk</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Murine norovirus GV</name>
        <supramolecule_list>
            <virus_supramolecule supramolecule_id="1">
                <name>Murine norovirus GV</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="463708">Murine norovirus GV</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                </natural_host>
                <virus_shell shell_id="1">
                    <diameter units="Å">400.0</diameter>
                    <triangulation>3</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>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Major capsid protein VP1</name>
                <natural_source database="NCBI">
                    <organism ncbi="1028322">Murine norovirus GV/NIH-2410/2005/USA</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.058833785</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="274590">Baculovirus expression vector pFastBac1-HM</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MRMSDGAAPKANGSEASGQDLVPTAVEQAVPIQPVAGAALAAPAAGQINQIDPWIFQNFVQCPLGEFSISPRNTPGEILF
DLALGPGLNPYLAHLSAMYTGWVGNMEVQLVLAGNAFTAGKVVVALVPPYFPKGSLTTAQITCFPHVMCDVRTLEPIQLP
LLDVRRVLWHATQDQEESMRLVCMLYTPLRTNSPGDESFVVSGRLLSKPAADFNFVYLTPPIERTIYRMVDLPVLQPRLC
THARWPAPIYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPVSGSWVSCFAAEAAYEFQSGIGEVATFTLIEQDGSAYVPG
DRAAPLGYPDFSGQLEIEVQTETTKKGEKLKVTTFEMILGPTTNVDQVPYQGRVYASLTAAASLDLVDGRVRAVPRSVYG
FQDVVPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDSTDAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNT
LTGQLLFECKLYSEGYIALSYSGSGPLTFPTDGFFEVVSWVPRLYQLASVGSLATGRTLKQ</string>
                    <external_references type="UNIPROTKB">B7XA03</external_references>
                </sequence>
            </protein_or_peptide>
        </macromolecule_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>7.4</ph>
                    </buffer>
                    <sugar_embedding>
                        <material>amorphous ice</material>
                    </sugar_embedding>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">0.1</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.5</nominal_defocus_max>
                    <nominal_magnification>75000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">76.0</temperature_min>
                        <temperature_max units="K">77.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <basic/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">4096</width>
                                    <height units="pixel">4096</height>
                                </dimensions>
                                <frames_per_image>3-31</frames_per_image>
                            </digitization_details>
                            <number_real_images>2746</number_real_images>
                            <average_exposure_time units="s">2.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">40.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">3.5</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                    <number_images_used>41847</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.0</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="864001">
        <file>emd_9741.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>600</col>
            <row>600</row>
            <sec>600</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>600</x>
            <y>600</y>
            <z>600</z>
        </spacing>
        <cell>
            <a units="Å">516.0</a>
            <b units="Å">516.0</b>
            <c units="Å">516.0</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>-0.08431751</minimum>
            <maximum>0.15500742</maximum>
            <average>0.0012706635</average>
            <std>0.007721407</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">0.86</x>
            <y units="Å">0.86</y>
            <z units="Å">0.86</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.035</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-9741::::</label>
        <annotation_details>Cryo-EM map of MNV-S7 VLP</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
                <overall_bvalue>157.0</overall_bvalue>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
