<emd emdb_id="EMD-3236" 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>2015-11-09</deposition>
            <header_release>2015-11-18</header_release>
            <map_release>2015-12-23</map_release>
            <update>2016-08-24</update>
        </key_dates>
        <title>Electron cryo-microscopy of filamentous flexible virus PepMV (Pepino Mosaic Virus)</title>
        <authors_list>
            <author>Agirrezabala X</author>
            <author>Mendez-Lopez E</author>
            <author>Lasso G</author>
            <author>Sanchez-Pina MA</author>
            <author>Aranda MA</author>
            <author>Valle M</author>
        </authors_list>
        <keywords>PepMV, filamentous plant virus, Potexvirus, helical symmetry</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Agirrezabala X</author>
                    <author order="2">Mendez-Lopez E</author>
                    <author order="3">Lasso G</author>
                    <author order="4">Sanchez-Pina MA</author>
                    <author order="5">Aranda MA</author>
                    <author order="6">Valle M</author>
                    <title>The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses</title>
                    <journal>eLife</journal>
                    <volume>4</volume>
                    <first_page>e11795</first_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26673077</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.11795</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5fn1</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Pepino Mosaic Virus, PepMV</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Pepino Mosaic Virus, PepMV</name>
                <oligomeric_state>Helical symmetry</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">35</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name>Pepino mosaic virus</name>
                <sci_species_name ncbi="112229">Pepino mosaic virus</sci_species_name>
                <sci_species_strain>PepMV-Sp13</sci_species_strain>
                <natural_host database="NCBI">
                    <organism ncbi="4081">Solanum lycopersicum</organism>
                    <synonym_organism>PLANTAE(HIGHER PLANTS)</synonym_organism>
                </natural_host>
                <host_system database="NCBI">
                    <recombinant_organism ncbi="4100">Nicotiana benthamiana</recombinant_organism>
                </host_system>
                <molecular_weight>
                    <theoretical units="MDa">35</theoretical>
                </molecular_weight>
                <virus_type>VIRION</virus_type>
                <virus_isolate>STRAIN</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">2</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>100 mM Tris-citric acid</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R 2/2 holey carbon grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK II</instrument>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_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>
                    <nominal_cs units="mm">2.7</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>
                    <calibrated_magnification>102987.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2014-02-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <number_real_images>100</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                            <details>Every image is the average of 25 frames recorded by direct electron detector</details>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>Spring software used</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">3.95</delta_z>
                            <delta_phi units="deg">41.1</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.9</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Spring, EMAN2, CTFTILT</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>Each partcile phase flipping</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="9904">
        <file>emd_3236.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>130</col>
            <row>130</row>
            <sec>150</sec>
        </dimensions>
        <origin>
            <col>-64</col>
            <row>-64</row>
            <sec>-74</sec>
        </origin>
        <spacing>
            <x>130</x>
            <y>130</y>
            <z>150</z>
        </spacing>
        <cell>
            <a units="&#8491;">176.8</a>
            <b units="&#8491;">176.8</b>
            <c units="&#8491;">204.0</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>-3.56212592</minimum>
            <maximum>5.79709911</maximum>
            <average>0.00825807</average>
            <std>0.77862281</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.36</x>
            <y units="&#8491;">1.36</y>
            <z units="&#8491;">1.36</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>CryoEM map of PepMV, a Potexvirus.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3236::::</details>
    </map>
</emd>