<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_11_7/emdb.xsd" version="3.0.11.7" emdb_id="EMD-80320">
    <admin>
        <current_status>
            <date>2026-09-02</date>
            <code>REL</code>
            <processing_site>PDBc</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2026-09-02">
                <change_list>
                    <model>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </model>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBc</last_processing>
        </sites>
        <key_dates>
            <deposition>2026-04-15</deposition>
            <header_release>2026-09-02</header_release>
            <map_release>2026-09-02</map_release>
            <update>2026-09-02</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Science Foundation (NSF, China)</funding_body>
                <country>China</country>
            </grant_reference>
        </grant_support>
        <title>CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS045</title>
        <authors_list>
            <author>Chen SD</author>
            <author>Li X</author>
        </authors_list>
        <keywords>Shiga toxin B subunit, Antibody, TOXIN/IMMUNE SYSTEM, TOXIN-IMMUNE SYSTEM complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author ORCID="0000-0002-7634-2141" order="1">Chen SD</author>
                    <author ORCID="0009-0008-7257-6240" order="2">Li X</author>
                    <title>CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising RDS045(pentamer)</title>
                    <journal_abbreviation>To Be Published</journal_abbreviation>
                    <external_references type="CSD">0353</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>25rg</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
        <other_db_list>
            <db_reference>
                <db_name>EMDB</db_name>
                <accession_id>EMD-80320</accession_id>
                <content_type>associated EM volume</content_type>
                <details>CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS045</details>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>Complex of Shiga toxin 1a B subunit and RDS045 Fab</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Complex of Shiga toxin 1a B subunit and RDS045 Fab</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Shiga toxin subunit B</name>
                <natural_source database="NCBI">
                    <organism ncbi="622">Shigella dysenteriae</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.008031011999999999</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MTPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFRGSG</string>
                    <external_references type="UNIPROTKB">Q32GM0</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Heavy chain of RDS045 Fab</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023474153999999997</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="10029">Cricetulus griseus</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>QVQLVQSGAEVKKPGASVKVSCKTSGYSFTDYYIHWIRQAPGQGLEWMGWINPNSGHTDFAHNFQGRVIMTRDTSISTAS
MELSGLTSDDTAVYYCTRVPGITEVDEDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVS
WNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>Light chain of RDS045 Fab</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023650344</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="10029">Cricetulus griseus</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>EIVLTQSPATLSLSPGDRATFSCRASQTVSGYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTEFTLTISSLEP
EDVAVYYCQHRSNWPLMCTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC</string>
                </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">
                    <buffer>
                        <ph>8.0</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>TFS 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="µm">1.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>TFS FALCON 4i (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/Å^2">55.0</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>
                <ctf_correction>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">2.5</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>cryoSPARC</name>
                        </software>
                    </software_list>
                    <number_images_used>825199</number_images_used>
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                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                </initial_angle_assignment>
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                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
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                <image_recording_id>1</image_recording_id>
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                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
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                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <file>emd_80320.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
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            <a units="Å">295.19998</a>
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        <label>::::EMDATABANK.org::::EMD-80320::::</label>
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