<?xml version="1.0" encoding="UTF-8"?>
<emdEntry accessCode="6257" version="1.9.6">
    <admin>
        <lastUpdate>2016-07-20</lastUpdate>
    </admin>
    <deposition>
        <status prior="HPUB">OBS</status>
        <depositionDate>2015-01-24</depositionDate>
        <depositionSite>RCSB</depositionSite>
        <processingSite>RCSB</processingSite>
        <headerReleaseDate>2015-03-18</headerReleaseDate>
        <obsoletedDate>2016-07-20</obsoletedDate>
        <details>Map for this entry will not be released.</details>
        <title>Cryo-EM structure of Dengue virus serotype 1 complexed with Fab fragments of human antibody D11C</title>
        <authors>Dip PV, Fibriansah G, Ng TS, Wang J, Kukkaro P, Kostyuchenko VA, Robinson JE, Isern S, Michael SF, Anand G, Schieffelin JS, Lok SM</authors>
        <keywords>antibody, Dengue virus, fusion loop</keywords>
        <fittedPDBEntryIdList>
            <fittedPDBEntryId>3j9h</fittedPDBEntryId>
        </fittedPDBEntryIdList>
        <primaryReference published="false">
            <journalArticle>
                <authors>Dip PV, Fibriansah G, Ng TS, Wang J, Kukkaro P, Kostyuchenko VA, Robinson JE, Isern S, Michael SF, Anand G, Schieffelin JS, Lok SM</authors>
                <articleTitle>Antibody-Dengue virus complex shows neutralization mechanism by the pre-dominant human antibodies</articleTitle>
                <journal>To Be Published</journal>
                <volume/>
                <firstPage/>
                <lastPage/>
                <year/>
            </journalArticle>
        </primaryReference>
    </deposition>
    <map>
        <file format="CCP4" sizeKb="524289" type="map">emd_6257.map.gz</file>
        <dataType>Image stored as Reals</dataType>
        <dimensions>
            <numColumns>512</numColumns>
            <numRows>512</numRows>
            <numSections>512</numSections>
        </dimensions>
        <origin>
            <originCol>-256</originCol>
            <originRow>-256</originRow>
            <originSec>-256</originSec>
        </origin>
        <limit>
            <limitCol>255</limitCol>
            <limitRow>255</limitRow>
            <limitSec>255</limitSec>
        </limit>
        <spacing>
            <spacingCol>512</spacingCol>
            <spacingRow>512</spacingRow>
            <spacingSec>512</spacingSec>
        </spacing>
        <cell>
            <cellA units="A">875.52</cellA>
            <cellB units="A">875.52</cellB>
            <cellC units="A">875.52</cellC>
            <cellAlpha units="degrees">90.0</cellAlpha>
            <cellBeta units="degrees">90.0</cellBeta>
            <cellGamma units="degrees">90.0</cellGamma>
        </cell>
        <axisOrder>
            <axisOrderFast>X</axisOrderFast>
            <axisOrderMedium>Y</axisOrderMedium>
            <axisOrderSlow>Z</axisOrderSlow>
        </axisOrder>
        <statistics>
            <minimum>-10.19386959</minimum>
            <maximum>16.27508354</maximum>
            <average>-0.13167311</average>
            <std>1.00621843</std>
        </statistics>
        <spaceGroupNumber>1</spaceGroupNumber>
        <details>::::EMDATABANK.org::::EMD-6257::::</details>
        <pixelSpacing>
            <pixelX units="A">1.71</pixelX>
            <pixelY units="A">1.71</pixelY>
            <pixelZ units="A">1.71</pixelZ>
        </pixelSpacing>
        <contourLevel source="author">1.5</contourLevel>
        <annotationDetails>Cryo-EM structure of Dengue virus serotype 1 complexed with variable region of Fab fragments of human antibody D11C</annotationDetails>
    </map>
    <supplement>
        <maskSet/>
        <sliceSet/>
        <figureSet/>
        <fscSet/>
    </supplement>
    <sample>
        <numComponents>2</numComponents>
        <name>Dengue virus serotype 1 with variable domain of Fab fragments of human monoclonal antibody D11C</name>
        <compDegree>60 Fab molecules bind to one Dengue virion</compDegree>
        <sampleComponentList>
            <sampleComponent componentID="1">
                <entry>virus</entry>
                <sciName>Dengue virus 1</sciName>
                <virus>
                    <sciSpeciesName ncbiTaxId="11053">Dengue virus 1</sciSpeciesName>
                    <sciSpeciesStrain>PVP159</sciSpeciesStrain>
                    <enveloped>true</enveloped>
                    <empty>false</empty>
                    <class>VIRION</class>
                    <isolate>STRAIN</isolate>
                    <externalReferences/>
                    <natSource>
                        <hostCategory>INVERTEBRATES</hostCategory>
                        <hostSpecies ncbiTaxId="7159">Aedes aegypti</hostSpecies>
                    </natSource>
                    <engSource>
                        <expSystem ncbiTaxId="7160">Aedes albopictus</expSystem>
                        <expSystemCell>C6/36 cells</expSystemCell>
                    </engSource>
                </virus>
            </sampleComponent>
            <sampleComponent componentID="2">
                <entry>protein</entry>
                <sciName>antibody D11C Fab, variable region</sciName>
                <protein>
                    <recombinantExpFlag>false</recombinantExpFlag>
                    <numCopies>60</numCopies>
                    <sciSpeciesName ncbiTaxId="9606">Homo sapiens</sciSpeciesName>
                    <synSpeciesName>human</synSpeciesName>
                    <externalReferences/>
                    <natSource/>
                    <engSource/>
                </protein>
            </sampleComponent>
        </sampleComponentList>
    </sample>
    <experiment>
        <vitrification>
            <method>Blot with filter paper for 2 seconds before plunging.</method>
            <cryogenName>ETHANE</cryogenName>
            <humidity>100</humidity>
            <instrument>FEI VITROBOT MARK IV</instrument>
            <temperature units="Kelvin">100</temperature>
        </vitrification>
        <imaging>
            <electronSource>FIELD EMISSION GUN</electronSource>
            <electronDose units="e/A**2">18.1</electronDose>
            <energyFilter>FEI</energyFilter>
            <imagingMode>BRIGHT FIELD</imagingMode>
            <nominalDefocusMin units="nm">1000</nominalDefocusMin>
            <nominalDefocusMax units="nm">4000</nominalDefocusMax>
            <illuminationMode>SPOT SCAN</illuminationMode>
            <detector>FEI FALCON I (4k x 4k)</detector>
            <nominalCs units="mm">2.7</nominalCs>
            <temperature units="Kelvin">100</temperature>
            <microscope>FEI TITAN KRIOS</microscope>
            <date>10-AUG-2013</date>
            <specimenHolderModel>FEI TITAN KRIOS AUTOGRID HOLDER</specimenHolderModel>
            <acceleratingVoltage units="kV">300</acceleratingVoltage>
            <nominalMagnification>47000</nominalMagnification>
        </imaging>
        <imageAcquisition/>
        <fitting>
            <software>O, Chimera, MDFF</software>
            <refProtocol>flexible</refProtocol>
            <refSpace>REAL</refSpace>
            <pdbEntryIdList>
                <pdbEntryId>1OAN</pdbEntryId>
            </pdbEntryIdList>
        </fitting>
        <specimenPreparation>
            <specimenState>particle</specimenState>
            <buffer>
                <details>12 mM Tris-HCl, pH 8.0, 120 mM NaCl, 1 mM EDTA</details>
                <ph>8.0</ph>
            </buffer>
        </specimenPreparation>
    </experiment>
    <processing>
        <method>singleParticle</method>
        <reconstruction>
            <algorithm>Cross-common lines</algorithm>
            <software>EMAN2, RELION, MPSA</software>
            <ctfCorrection>Each particle</ctfCorrection>
            <resolutionByAuthor>21</resolutionByAuthor>
            <resolutionMethod>FSC 0.5, semi-independent</resolutionMethod>
        </reconstruction>
        <singleParticle>
            <numClassAverages>100</numClassAverages>
            <appliedSymmetry>I</appliedSymmetry>
            <numProjections>8537</numProjections>
            <details>The particles were selected manually.</details>
        </singleParticle>
    </processing>
</emdEntry>
