<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-27357">
    <admin>
        <current_status>
            <date>2023-07-19</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-06-19</deposition>
            <header_release>2023-06-21</header_release>
            <map_release>2023-06-21</map_release>
            <update>2023-07-19</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>AI136621</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <code>INV-004923</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Bill &amp; Melinda Gates Foundation</funding_body>
                <code>INV-002916</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>nsEM map of hemagglutinin H3 A/Sing/INFIMH/16 complexed with polyclonal Fab samples from individual 182419 at day 2</title>
        <authors_list>
            <author ORCID="0000-0001-5598-1780">Torrents de la Pena A</author>
            <author ORCID="0000-0002-2020-2991">Sewall LM</author>
            <author ORCID="0000-0001-7153-3769">Ward AB</author>
        </authors_list>
        <keywords>influenza, H3, nsEM, EMPEM, VIRAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Torrents de la Pena A</author>
                    <author order="2">Sewall LM</author>
                    <author order="3">de Paiva Froes Rocha R</author>
                    <author order="4">Jackson AM</author>
                    <author order="5">Pratap PP</author>
                    <author order="6">Bangaru S</author>
                    <author order="7">Cottrell CA</author>
                    <author order="8">Mohanty S</author>
                    <author order="9">Shaw AC</author>
                    <author order="10">Ward AB</author>
                    <title>Increasing sensitivity of antibody-antigen interactions using photo-cross-linking.</title>
                    <journal_abbreviation>Cell Rep Methods</journal_abbreviation>
                    <volume>3</volume>
                    <first_page>100509</first_page>
                    <last_page>100509</last_page>
                    <year>2023</year>
                    <external_references type="PUBMED">37426749</external_references>
                    <external_references type="DOI">doi:10.1016/j.crmeth.2023.100509</external_references>
                    <external_references type="ISSN">2667-2375</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>nsEM map of hemagglutinin H1 A/Mich/045/15 complexed with polyclonal Fab samples from individual 182419 at day 0</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>nsEM map of hemagglutinin H1 A/Mich/045/15 complexed with polyclonal Fab samples from individual 182419 at day 0</name>
                <parent>0</parent>
                <details>HA recombinantly expressed in HEK 293F cells 
Fab samples isolated from several individuals at different timepoints</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_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">0.02</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <component>
                            <concentration units="0.020">0.02</concentration>
                            <formula>TBS</formula>
                            <name>Tris-buffered saline</name>
                        </component>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <material>Uranyl Formate</material>
                    </staining>
                    <grid>
                        <model>EMS Lacey Carbon</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                        </support_film>
                    </grid>
                    <details>15 ug of H1 A/Mich15/045/15 was complexed overnight with 500 ug of polyclonal Fab samples and SEC purified. The complex peak was concentrated to ~0.02 mg/ml and imaged</details>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI SPIRIT</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <c2_aperture_diameter units="µm">70.0</c2_aperture_diameter>
                    <nominal_defocus_min units="µm">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>52000.0</nominal_magnification>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>FEI EAGLE (4k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <average_electron_dose_per_image units="e/Å^2">50.0</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>
                <particle_selection>
                    <number_selected>146381</number_selected>
                </particle_selection>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>4M4Y</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">25.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <number_images_used>49464</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <details>bayesian polishing</details>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>OTHER</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>3.0</version>
                        </software>
                    </software_list>
                    <details>bayesian polishing</details>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16385">
        <file>emd_27357.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="Å">329.59998</a>
            <b units="Å">329.59998</b>
            <c units="Å">329.59998</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>-0.022646135</minimum>
            <maximum>0.081161916</maximum>
            <average>0.00016571517</average>
            <std>0.0042412165</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.06</x>
            <y units="Å">2.06</y>
            <z units="Å">2.06</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-27357::::</label>
        <annotation_details>nsEM map of hemagglutinin H3 A/Sing/INFIMH/16 complexed with polyclonal Fab samples from individual 182419 at day 2</annotation_details>
    </map>
    <interpretation>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="16385">
                <file>emd_27357_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>160</col>
                    <row>160</row>
                    <sec>160</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>160</x>
                    <y>160</y>
                    <z>160</z>
                </spacing>
                <cell>
                    <a units="Å">329.59998</a>
                    <b units="Å">329.59998</b>
                    <c units="Å">329.59998</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>-0.023794724</minimum>
                    <maximum>0.08255548</maximum>
                    <average>0.00016636218</average>
                    <std>0.004307491</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.06</x>
                    <y units="Å">2.06</y>
                    <z units="Å">2.06</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-27357::::</label>
                <annotation_details>nsEM half map of hemagglutinin H3 A/Sing/INFIMH/16 complexed with polyclonal Fab samples from individual 182419 at day 2</annotation_details>
            </half_map>
            <half_map format="CCP4" size_kbytes="16385">
                <file>emd_27357_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>160</col>
                    <row>160</row>
                    <sec>160</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>160</x>
                    <y>160</y>
                    <z>160</z>
                </spacing>
                <cell>
                    <a units="Å">329.59998</a>
                    <b units="Å">329.59998</b>
                    <c units="Å">329.59998</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>-0.025033472</minimum>
                    <maximum>0.08245499</maximum>
                    <average>0.00016771445</average>
                    <std>0.004311343</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">2.06</x>
                    <y units="Å">2.06</y>
                    <z units="Å">2.06</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-27357::::</label>
                <annotation_details>nsEM half map of hemagglutinin H3 A/Sing/INFIMH/16 complexed with polyclonal Fab samples from individual 182419 at day 2</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
