<?xml version="1.0" encoding="UTF-8"?>
<emdEntry accessCode="3230" version="1.9.6">
    <admin>
        <lastUpdate>2017-05-03</lastUpdate>
    </admin>
    <deposition>
        <status prior="HPUB">OBS</status>
        <depositionDate>2015-11-04</depositionDate>
        <depositionSite>PDBe</depositionSite>
        <processingSite>PDBe</processingSite>
        <headerReleaseDate>2015-11-18</headerReleaseDate>
        <mapReleaseDate>2017-05-03</mapReleaseDate>
        <obsoletedDate>2017-05-03</obsoletedDate>
        <supersededByList>
            <entry>EMD-4060</entry>
        </supersededByList>
        <details>map is obsoleate</details>
        <title>Negative Stain electron microscopy of GIF:IL2 complex</title>
        <authors>Felix J, Kandiah E, van Zundert GCP, Pauwels K, Novanska K, Verstraete K, Bloch Y, Read RJ, Vergauwen B, Gutsche I, Savvides SN</authors>
        <keywords>immune system, ORF virus, cytokines, cytokine receptors</keywords>
        <primaryReference published="true">
            <journalArticle>
                <authors>Felix J, Kandiah E, De Munck S, Bloch Y, van Zundert GC, Pauwels K, Dansercoer A, Novanska K, Read RJ, Bonvin AM, Vergauwen B, Verstraete K, Gutsche I, Savvides SN</authors>
                <articleTitle>Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF</articleTitle>
                <journal>Nat. comm.</journal>
                <volume>n/a</volume>
                <firstPage>13228</firstPage>
                <lastPage>n/a</lastPage>
                <year>2016</year>
                <externalReference type="pubmed">27819269</externalReference>
                <externalReference type="doi">doi:10.1038/ncomms13228</externalReference>
            </journalArticle>
        </primaryReference>
    </deposition>
    <map>
        <file format="CCP4" sizeKb="1025" type="map">emd_3230.map.gz</file>
        <dataType>Image stored as Reals</dataType>
        <dimensions>
            <numColumns>64</numColumns>
            <numRows>64</numRows>
            <numSections>64</numSections>
        </dimensions>
        <origin>
            <originCol>0</originCol>
            <originRow>0</originRow>
            <originSec>0</originSec>
        </origin>
        <limit>
            <limitCol>63</limitCol>
            <limitRow>63</limitRow>
            <limitSec>63</limitSec>
        </limit>
        <spacing>
            <spacingCol>64</spacingCol>
            <spacingRow>64</spacingRow>
            <spacingSec>64</spacingSec>
        </spacing>
        <cell>
            <cellA units="A">224.0</cellA>
            <cellB units="A">224.0</cellB>
            <cellC units="A">224.0</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>-0.03177558</minimum>
            <maximum>0.10385541</maximum>
            <average>0.00035476</average>
            <std>0.00756786</std>
        </statistics>
        <spaceGroupNumber>1</spaceGroupNumber>
        <details>::::EMDATABANK.org::::EMD-3230::::</details>
        <pixelSpacing>
            <pixelX units="A">3.5</pixelX>
            <pixelY units="A">3.5</pixelY>
            <pixelZ units="A">3.5</pixelZ>
        </pixelSpacing>
        <contourLevel source="author">0.018</contourLevel>
        <annotationDetails>Negative Stain Reconstruction of GIF:IL2 complex</annotationDetails>
    </map>
    <supplement>
        <maskSet/>
        <sliceSet/>
        <figureSet/>
        <fscSet/>
    </supplement>
    <sample>
        <numComponents>2</numComponents>
        <name>Complex of GIF:IL2</name>
        <compDegree>4:2 stoichiometry</compDegree>
        <molWtMethod>SEC-MALLS</molWtMethod>
        <molWtExp units="MDa">0.163</molWtExp>
        <sampleComponentList>
            <sampleComponent componentID="1">
                <entry>protein</entry>
                <sciName>orf virus GM-CSF/IL-2 Inhibition Factor</sciName>
                <synName>GIF</synName>
                <molWtExp units="MDa">0.101</molWtExp>
                <protein>
                    <numCopies>4</numCopies>
                    <oligomericDetails>tetramer</oligomericDetails>
                    <sciSpeciesStrain>NZ-2</sciSpeciesStrain>
                    <sciSpeciesName ncbiTaxId="10258">Orf virus</sciSpeciesName>
                    <recombinantExpFlag>true</recombinantExpFlag>
                    <externalReferences>
                        <refUniProt>Q9J5U5</refUniProt>
                        <refInterpro>IPR003184</refInterpro>
                    </externalReferences>
                    <natSource/>
                    <engSource>
                        <expSystemCell>HEK293T</expSystemCell>
                        <expSystemStrain>HEK293T</expSystemStrain>
                        <vector>pHLsec</vector>
                    </engSource>
                </protein>
            </sampleComponent>
            <sampleComponent componentID="2">
                <entry>protein</entry>
                <sciName>Ovine Interleukin-2</sciName>
                <synName>ovine IL-2</synName>
                <molWtExp units="MDa">0.0219</molWtExp>
                <protein>
                    <oligomericDetails>monomer</oligomericDetails>
                    <recombinantExpFlag>true</recombinantExpFlag>
                    <numCopies>1</numCopies>
                    <sciSpeciesName ncbiTaxId="9940">Ovis aries</sciSpeciesName>
                    <synSpeciesName>Ovine</synSpeciesName>
                    <externalReferences>
                        <refInterpro>IPR009079</refInterpro>
                        <refInterpro>IPR012351</refInterpro>
                        <refInterpro>IPR000779</refInterpro>
                        <refInterpro>IPR030477</refInterpro>
                        <refUniProt>P19114</refUniProt>
                        <refGo>GO:0005615</refGo>
                        <refGo>GO:0002250</refGo>
                    </externalReferences>
                    <natSource/>
                    <engSource>
                        <vector>pHLsec</vector>
                        <expSystemCell>HEK293T</expSystemCell>
                        <expSystemStrain>HEK293T</expSystemStrain>
                    </engSource>
                </protein>
            </sampleComponent>
        </sampleComponentList>
    </sample>
    <experiment>
        <vitrification>
            <cryogenName>NONE</cryogenName>
            <instrument>NONE</instrument>
        </vitrification>
        <imaging>
            <electronSource>LAB6</electronSource>
            <imagingMode>BRIGHT FIELD</imagingMode>
            <temperatureMin units="Kelvin">294</temperatureMin>
            <illuminationMode>FLOOD BEAM</illuminationMode>
            <details>Low-dose mode</details>
            <detector>KODAK SO-163 FILM</detector>
            <nominalCs units="mm">2</nominalCs>
            <microscope>JEOL 1200EXII</microscope>
            <date>01-OCT-2013</date>
            <specimenHolderModel>OTHER</specimenHolderModel>
            <acceleratingVoltage units="kV">100</acceleratingVoltage>
            <nominalMagnification>40000</nominalMagnification>
        </imaging>
        <imageAcquisition>
            <scanner>ZEISS SCAI</scanner>
            <numDigitalImages>26</numDigitalImages>
            <samplingSize units="microns">7</samplingSize>
            <quantBitNumber>8</quantBitNumber>
        </imageAcquisition>
        <fitting/>
        <specimenPreparation>
            <staining>Sample was applied to the clear side of carbon on a carbon-mica interface and stained with 2 % (w/v) uranyl acetate.</staining>
            <specimenState>particle</specimenState>
        </specimenPreparation>
    </experiment>
    <processing>
        <method>singleParticle</method>
        <reconstruction>
            <algorithm>Projection-matching</algorithm>
            <software>RELION, VIPER</software>
            <ctfCorrection>each particle</ctfCorrection>
            <details>final map was filtered to 25A</details>
            <resolutionByAuthor>19</resolutionByAuthor>
            <resolutionMethod>FSC 0.143, gold-standard</resolutionMethod>
        </reconstruction>
        <singleParticle>
            <appliedSymmetry>C2</appliedSymmetry>
            <numProjections>31675</numProjections>
            <details>E2BOXER, RELION, VIPER</details>
        </singleParticle>
    </processing>
</emdEntry>
