<emd emdb_id="EMD-6611" 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>2016-02-29</deposition>
            <header_release>2016-03-30</header_release>
            <map_release>2016-03-30</map_release>
            <update>2016-04-13</update>
        </key_dates>
        <title>Cryo-electron microscopy structure of chimeric influenza cH5/1 hemagglutinin bound to stalk-targeting antibody, 6F12</title>
        <authors_list>
            <author>Tran EEH</author>
            <author>Podolsky KA</author>
            <author>Bartesaghi A</author>
            <author>Kuybeda O</author>
            <author>Grandinetti G</author>
            <author>Wohlbold TJ</author>
            <author>Tan GS</author>
            <author>Nachbagauer R</author>
            <author>Palese P</author>
            <author>Krammer F</author>
            <author>Subramaniam S</author>
        </authors_list>
        <keywords>Influenza, chimeric HA, universal vaccine candidate</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Tran EEH</author>
                    <author order="2">Podolsky KA</author>
                    <author order="3">Bartesaghi A</author>
                    <author order="4">Kuybeda O</author>
                    <author order="5">Grandinetti G</author>
                    <author order="6">Wohlbold TJ</author>
                    <author order="7">Tan GS</author>
                    <author order="8">Nachbagauer R</author>
                    <author order="9">Palese P</author>
                    <author order="10">Krammer F</author>
                    <author order="11">Subramaniam S</author>
                    <title>Cryo-electron Microscopy Structures of Chimeric Hemagglutinin Displayed on a Universal Vaccine Candidate</title>
                    <journal>mBio</journal>
                    <volume>7</volume>
                    <year>2016</year>
                    <external_references type="PUBMED">27006464</external_references>
                    <external_references type="DOI">doi:10.1128/mBio.00257-16</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-6607</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
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            <emdb_reference>
                <emdb_id>EMD-6608</emdb_id>
                <relationship>
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            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-6609</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-6610</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-6612</emdb_id>
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            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-6613</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-6614</emdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
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    <sample>
        <name>Tomographic subvolume average of virus-bound influenza cH5/1 HA in complex with the stalk-binding antibody, 6F12</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Tomographic subvolume average of virus-bound influenza cH5/1 HA in complex with the stalk-binding antibody, 6F12</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>cH5/1 hemagglutinin</name>
                <natural_source database="NCBI">
                    <organism ncbi="11309">unidentified influenza virus</organism>
                    <strain>cH5/1N1</strain>
                </natural_source>
                <oligomeric_state>trimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Immunoglobulin 6F12</name>
                <natural_source database="NCBI">
                    <organism ncbi="10090">Mus musculus</organism>
                    <strain>BALB/c</strain>
                    <synonym_organism>Mouse</synonym_organism>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>subtomogramAveraging</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <subtomogram_averaging_preparation preparation_id="1">
                    <buffer>
                        <ph>7.4</ph>
                        <details>25 mM Tris, 100 mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil Multi-A 200 mesh carbon grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                        <timed_resolved_state>Virus was incubated with antibody for ~30 minutes on ice before solution was plunge-frozen</timed_resolved_state>
                        <method>Blot for 6 seconds before plunging.</method>
                    </vitrification>
                </subtomogram_averaging_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <subtomogram_averaging_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_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>64000.0</nominal_magnification>
                    <calibrated_magnification>23000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>Gatan, Inc.</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2015-04-16</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <number_real_images>10</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">120</average_electron_dose_per_image>
                            <details>Every image is the average of four frames recorded by the direct electron detector.</details>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Liquid nitrogen-cooled</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                        </axis1>
                    </tilt_series>
                </subtomogram_averaging_microscopy>
            </microscopy_list>
            <subtomogram_averaging_processing image_processing_id="1">
                <details>Subtomograms were selected using an automatic selection program.</details>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">25.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_subtomograms_used>134</number_subtomograms_used>
                </final_reconstruction>
            </subtomogram_averaging_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_6611.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>49</col>
            <row>49</row>
            <sec>99</sec>
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            <col>0</col>
            <row>0</row>
            <sec>0</sec>
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        <spacing>
            <x>49</x>
            <y>49</y>
            <z>99</z>
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        <cell>
            <a units="&#8491;">200.9</a>
            <b units="&#8491;">200.9</b>
            <c units="&#8491;">405.9</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>-0.24462633</minimum>
            <maximum>0.47881263</maximum>
            <average>-0.00037731</average>
            <std>0.05479031</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">4.1</x>
            <y units="&#8491;">4.1</y>
            <z units="&#8491;">4.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.115</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Tomographic subvolume average of virus-bound influenza cH5/1 HA in complex with the stalk-binding antibody, 6F12</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6611::::</details>
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    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6611.png</file>
            </figure>
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