<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-8548">
    <admin>
        <current_status>
            <date>2024-11-13</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-01-12</deposition>
            <header_release>2017-03-29</header_release>
            <map_release>2017-03-29</map_release>
            <update>2024-11-13</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>AI076331</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>AI073755</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>AI104972</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)</funding_body>
                <code>HHSN272201400024C</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>A Human Antibody Against Zika Virus Crosslinks the E Protein to Prevent Infection</title>
        <authors_list>
            <author>Hasan SS</author>
            <author>Miller A</author>
        </authors_list>
        <keywords>flavivirus, Zika, human antibody, therapeutic, VIRUS-IMMUNE SYSTEM complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Hasan SS</author>
                    <author order="2">Miller A</author>
                    <author order="3">Sapparapu G</author>
                    <author order="4">Fernandez E</author>
                    <author order="5">Klose T</author>
                    <author order="6">Long F</author>
                    <author order="7">Fokine A</author>
                    <author order="8">Porta JC</author>
                    <author order="9">Jiang W</author>
                    <author order="10">Diamond MS</author>
                    <author order="11">Crowe JE</author>
                    <author order="12">Kuhn RJ</author>
                    <author order="13">Rossmann MG</author>
                    <title>A human antibody against Zika virus crosslinks the E protein to prevent infection.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>8</volume>
                    <first_page>14722</first_page>
                    <last_page>14722</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">28300075</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms14722</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5uhy</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Zika virus with ZIKV117 Fab</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Zika virus with ZIKV117 Fab</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="64320">Zika virus</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>ZV67 Fab chain 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023658074</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQQKPGQSPKLLIYSASNRYTGVPDRFTGSGSGTDFTLTISNMQS
EDLADYFCQQFSSYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVL
NSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>ZV67 Fab chain 2</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023074841999999998</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>AQLQQSGTGLARPGASVKLSCKASGYTFTSYGISWVTQRAGQGLEWIGVIYPRSGNTYYNEKFRGKATLTADKSSSSAYM
ELRGLTAEDSAVYFCARENYGSVYWGQGTTLTVSSAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGS
LSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRVPI</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>envelope protein</name>
                <natural_source database="NCBI">
                    <organism ncbi="64320">Zika virus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.043123906000000004</theoretical>
                </molecular_weight>
                <number_of_copies>3</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="36483">Cricetinae gen. sp.</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEA
YLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHET
DENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKE
ALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAE
TLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKI</string>
                    <external_references type="UNIPROTKB">A0A120IIH7</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">
                    <concentration units="mg/mL">1</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">30.0</concentration>
                            <formula>C4H11NO3</formula>
                            <name>Trizma</name>
                        </component>
                        <component>
                            <concentration units="mM">120.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <name>EDTA</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Ted Pella 01824</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>LACEY</film_topology>
                        </support_film>
                        <details>no pretreatment</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">293</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <details>2.5 uL of sample was deposited on the carbon layer, with double-sided blotting applied twice for 5-6 seconds.. </details>
                    </vitrification>
                    <details>1 mg/mL E protein</details>
                </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>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_magnification>18000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3838</width>
                                    <height units="pixel">3710</height>
                                </dimensions>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>1140</number_real_images>
                            <average_exposure_time units="s">11.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">32.6</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="OTHER"/>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>I</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">6.2</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>jspr</name>
                        </software>
                    </software_list>
                    <number_images_used>8153</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>RANDOM ASSIGNMENT</type>
                    <software_list>
                        <software>
                            <name>jspr</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                    <software_list>
                        <software>
                            <name>jspr</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="322487">
        <file>emd_8548.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>432</col>
            <row>432</row>
            <sec>432</sec>
        </dimensions>
        <origin>
            <col>-216</col>
            <row>-216</row>
            <sec>-216</sec>
        </origin>
        <spacing>
            <x>432</x>
            <y>432</y>
            <z>432</z>
        </spacing>
        <cell>
            <a units="Å">699.84</a>
            <b units="Å">699.84</b>
            <c units="Å">699.84</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>-4.6381545</minimum>
            <maximum>9.6539345</maximum>
            <average>0.00082005863</average>
            <std>0.99996656</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.62</x>
            <y units="Å">1.62</y>
            <z units="Å">1.62</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.9</level>
                <source>EMDB</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-8548::::</label>
        <annotation_details>Zika virus-antibody complex</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
