<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-3229" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-11-04</deposition>
            <header_release>2015-11-18</header_release>
            <obsolete>2017-05-03</obsolete>
            <update>2017-05-03</update>
        </key_dates>
        <title>Negative Stain electron microscopy of GM-CSF:GIF complex</title>
        <authors_list>
            <author>Felix J</author>
            <author>Kandiah E</author>
            <author>van Zundert GCP</author>
            <author>Pauwels K</author>
            <author>Novanska K</author>
            <author>Verstraete K</author>
            <author>Bloch Y</author>
            <author>Read RJ</author>
            <author>Vergauwen B</author>
            <author>Gutsche I</author>
            <author>Savvides SN</author>
        </authors_list>
        <keywords>immune system, ORF virus, cytokines, cytokine receptors</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Felix J</author>
                    <author order="2">Kandiah E</author>
                    <author order="3">van Zundert GCP</author>
                    <author order="4">Pauwels K</author>
                    <author order="5">Novanska K</author>
                    <author order="6">Verstraete K</author>
                    <author order="7">Bloch Y</author>
                    <author order="8">Read RJ</author>
                    <author order="9">Vergauwen B</author>
                    <author order="10">Gutsche I</author>
                    <author order="11">Savvides SN</author>
                    <title>Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF to achieve immunomodulation</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Complex of GM-CSF:GIF</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Complex of GM-CSF:GIF</name>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.164</experimental>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="GIF">orf virus GM-CSF/IL-2 Inhibition Factor</name>
                <natural_source database="NCBI">
                    <organism ncbi="10258">Orf virus</organism>
                    <strain>NZ-2</strain>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.101</experimental>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <oligomeric_state>tetramer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_strain>HEK293T</recombinant_strain>
                    <recombinant_cell>HEK293T</recombinant_cell>
                    <recombinant_plasmid>pHLsec</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q9J5U5</external_references>
                    <external_references type="INTERPRO">IPR003184</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="ovine GM-CSF">ovine granulocyte macrophage colony-stimulating factor</name>
                <natural_source database="NCBI">
                    <organism ncbi="9940">Ovis aries</organism>
                    <synonym_organism>Ovine</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.0192</experimental>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_strain>HEK293T</recombinant_strain>
                    <recombinant_cell>HEK293T</recombinant_cell>
                    <recombinant_plasmid>pHLsec</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P28773</external_references>
                    <external_references type="GO">GO:0005615</external_references>
                    <external_references type="GO">GO:0001892</external_references>
                    <external_references type="GO">GO:0006955</external_references>
                    <external_references type="INTERPRO">IPR009079</external_references>
                    <external_references type="INTERPRO">IPR012351</external_references>
                    <external_references type="INTERPRO">IPR000773</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">
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Sample was applied to the clear side of carbon on a carbon-mica interface and stained with 2 % (w/v) uranyl acetate.</details>
                    </staining>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 1200EXII</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">100</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_magnification>40000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">294</temperature_min>
                    </temperature>
                    <details>Low-dose mode</details>
                    <date>2013-10-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>ZEISS SCAI</scanner>
                                <sampling_interval units="µm">7</sampling_interval>
                            </digitization_details>
                            <number_real_images>30</number_real_images>
                            <bits_per_pixel>8.0</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>E2BOXER, RELION, VIPER</details>
                <ctf_correction>
                    <details>each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">17.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION, VIPER</name>
                        </software>
                    </software_list>
                    <details>final map was filtered to 25A</details>
                    <number_images_used>24324</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="1025">
        <file>emd_3229.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>64</col>
            <row>64</row>
            <sec>64</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>64</x>
            <y>64</y>
            <z>64</z>
        </spacing>
        <cell>
            <a units="Å">224.0</a>
            <b units="Å">224.0</b>
            <c units="Å">224.0</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>-0.04944067</minimum>
            <maximum>0.10318178</maximum>
            <average>0.00030788</average>
            <std>0.00862715</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">3.5</x>
            <y units="Å">3.5</y>
            <z units="Å">3.5</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0286</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Negative Stain Reconstruction of GM-CSF:GIF complex</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3229::::</details>
    </map>
</emd>
