<emd emdb_id="EMD-6619" 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>2016-03-15</deposition>
            <header_release>2016-05-11</header_release>
            <map_release>2017-01-25</map_release>
            <update>2017-03-29</update>
        </key_dates>
        <title>Electron cryo-microscopy of Human Papillomavirus</title>
        <authors_list>
            <author>Guan J</author>
            <author>Bywaters SM</author>
            <author>Brendle SA</author>
            <author>Ashley RE</author>
            <author>Makhov AM</author>
            <author>Conway JF</author>
            <author>Christensen ND</author>
            <author>Hafenstein S</author>
        </authors_list>
        <keywords>DED high resolution map, L1 plus L2, quasivirus, Heparin</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Guan J</author>
                    <author order="2">Bywaters SM</author>
                    <author order="3">Brendle SA</author>
                    <author order="4">Ashley RE</author>
                    <author order="5">Makhov AM</author>
                    <author order="6">Conway JF</author>
                    <author order="7">Christensen ND</author>
                    <author order="8">Hafenstein S</author>
                    <title>Cryoelectron Microscopy Maps of Human Papillomavirus 16 Reveal L2 Densities and Heparin Binding Site.</title>
                    <journal>STRUCTURE</journal>
                    <volume>25</volume>
                    <first_page>253</first_page>
                    <last_page>263</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28065506</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2016.12.001</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5keq</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Human papillomavirus bound to heparin</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Human papillomavirus bound to heparin</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <virus_supramolecule supramolecule_id="1">
                <name synonym="HPV16">Human papillomavirus 16</name>
                <sci_species_name ncbi="337041">Human papillomavirus 16</sci_species_name>
                <natural_host database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>VERTEBRATES</synonym_organism>
                </natural_host>
                <host_system database="NCBI" />
                <virus_shell shell_id="1">
                    <name>L1 plus L2</name>
                    <diameter units="&#8491;">580</diameter>
                    <triangulation>7</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>HPV16</syn_species_name>
                <sci_species_serotype>HPV16</sci_species_serotype>
            </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">1.2</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>1 M NaCl, 200 mM Tris</details>
                    </buffer>
                    <grid>
                        <details>glow-discharged holey carbon support grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">102</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</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_magnification>93000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2015-01-20</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>6175</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>The particles were selected using semi-automatic program e2boxer.py.</details>
                <ctf_correction>
                    <details>ctffind for whole image</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.3</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>auto3dem</name>
                        </software>
                    </software_list>
                    <number_images_used>51422</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>10</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1164367">
        <file>emd_6619.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>668</col>
            <row>668</row>
            <sec>668</sec>
        </dimensions>
        <origin>
            <col>-334</col>
            <row>-334</row>
            <sec>-334</sec>
        </origin>
        <spacing>
            <x>668</x>
            <y>668</y>
            <z>668</z>
        </spacing>
        <cell>
            <a units="&#8491;">766.196</a>
            <b units="&#8491;">766.196</b>
            <c units="&#8491;">766.196</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>-10.35167027</minimum>
            <maximum>15.41951847</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.147</x>
            <y units="&#8491;">1.147</y>
            <z units="&#8491;">1.147</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of HPV16 complex with Heparin</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6619::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3OAE</access_code>
                </initial_model>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>3J6R</access_code>
                </initial_model>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>