<?xml version="1.0" encoding="UTF-8"?>
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    <admin>
        <current_status>
            <date>2025-10-29</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <revision_history>
            <revision version="1.0" date="2025-10-29">
                <change_list>
                    <model>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </model>
                    <metadata>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </metadata>
                    <fsc>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
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                    <half_map part="1">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </half_map>
                    <half_map part="2">
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
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                    <image>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </image>
                    <primary_map>
                        <revision_type>INITIAL_RELEASE</revision_type>
                        <provider>REPOSITORY</provider>
                    </primary_map>
                </change_list>
            </revision>
        </revision_history>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2024-10-23</deposition>
            <header_release>2025-10-29</header_release>
            <map_release>2025-10-29</map_release>
            <update>2025-10-29</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Not funded</funding_body>
            </grant_reference>
        </grant_support>
        <title>Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203</title>
        <authors_list>
            <author>Binshtein E</author>
            <author>Crowe JE</author>
        </authors_list>
        <keywords>PTx, mAb, Whooping, TOXIN, TOXIN-Immune System complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author ORCID="0000-0003-2745-104X" order="1">Binshtein E</author>
                    <author ORCID="0000-0002-0049-1079" order="2">Crowe JE</author>
                    <title>Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203</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>9e3l</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-47487</accession_id>
                <content_type>associated EM volume</content_type>
                <details>Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203</details>
            </db_reference>
        </other_db_list>
    </crossreferences>
    <sample>
        <name>pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203</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>
                        <macromolecule_id>4</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>5</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>6</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>7</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>8</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>9</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="520">Bordetella pertussis</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Pertussis toxin subunit 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="520">Bordetella pertussis</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.030005188</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="520">Bordetella pertussis</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MRCTRAIRQTARTGWLTWLAILAVTAPVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSCQVGSS
NSAFVSTSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTYGDNAGRILAGALATY
QSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQTRANPNPYTSRRSVASIVGTLVRMAPVVGACMARQA
ESSEAMAAWSERAGEAMVLVYYESIAYSF</string>
                    <external_references type="UNIPROTKB">T1SR96</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Islet-activating protein S2</name>
                <natural_source database="NCBI">
                    <organism ncbi="520">Bordetella pertussis</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.024856299</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="520">Bordetella pertussis</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MPIDRKTLCHLLSVLPLALLGSHVARASTPGIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWS
IFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGA
CTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC</string>
                    <external_references type="UNIPROTKB">A0A0E8DFW5</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>Pertussis toxin subunit 3</name>
                <natural_source database="NCBI">
                    <organism ncbi="520">Bordetella pertussis</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.025012819999999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="520">Bordetella pertussis</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MLINNKKLLHHILPILVLALLGMRTAQAVAPGIVIPPKALFTQQGGAYGRCPNGTRALTVAELRGNAELQTYLRQITPGW
SIYGLYDGTYLGQAYGGIIKDAPPGAGFIYRETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVFVRDGQSVIG
ACASPYEGRYRDMYDALRRLLYMIYMSGLAVRVHVSKEEQYYDYEDATFQTYALTGISLCNPAASIC</string>
                    <external_references type="UNIPROTKB">P04979</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name>Pertussis toxin subunit 4</name>
                <natural_source database="NCBI">
                    <organism ncbi="520">Bordetella pertussis</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.016566743999999998</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="520">Bordetella pertussis</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MLRRFPTRTTAPGQGGARRSRVRALAWLLASGAMTHLSPALADVPYVLVKTNMVVTSVAMKPYEVTPTRMLVCGIAAKLG
AAASSPDAHVPFCFGKDLKRPGSSPMEVMLRAVFMQQRPLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP</string>
                    <external_references type="UNIPROTKB">P0A3R5</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="5">
                <name>Pertussis toxin subunit 5</name>
                <natural_source database="NCBI">
                    <organism ncbi="520">Bordetella pertussis</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.014513754999999998</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="520">Bordetella pertussis</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MQRQAGLPLKANPMHTIASILLSVLGIYSPADVAGLPTHLYKNFTVQELALKLKGKNQEFCLTAFMSGRSLVRACLSDAG
HEHDTWFDTMLGFAISAYALKSRIALTVEDSPYPGTPGDLLELQICPLNGYCE</string>
                    <external_references type="UNIPROTKB">P04981</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="6">
                <name>PERT-203 HC</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.024581383000000002</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>QVQLQESGPGLVKPSGTLSLTCAVSGGSISSNDWWSWVRQSPGKGLEWIGESYHSGGTNYNPSLTSRVTISVDQSKNHFS
LRLSSVTAADTAVYFCARRTIGNYDISTGYYTPAVFFDSWGQGILVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="7">
                <name>PERT-203 LC</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.024143919999999996</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>DIVMTQSPLSLPVTPGEPASISCRSSQSLLHSNTYNYLDWYLQKPGQSPQLLIYLGSHRASGVPDRFSGSGSGTDFTLKI
SRVEAEDVGVYYCMQSLQTPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQ
SGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="8">
                <name>PERT-169 HC</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.024570528999999997</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>QVQLVQAGGEVKKPGTSVNVSCKASVYTFTNYYLHWVRQAPGQGLEWMGVMNPSGGKTIYAQKFQGRVTTTRDTSTSTVY
MELRSLRSEDTAVYYCARGLYYGDSSGYFGAGEFDHWGQGTLVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYF
PEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="9">
                <name>PERT-169 LC</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.022848446999999997</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>QAVVTQEPSLTVSPGGTVTLTCGSSTGAVTSGHYPFWLQQKPGQAPRTLIYDTSNKHSWTPARFSASLLGGKAALTLSGA
QPEDEAEYYCLLSYSGARRVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVK
AGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS</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>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.0</nominal_defocus_max>
                    <nominal_magnification>105000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <zemlin_tableau/>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Bioquantum</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K3 (6k x 4k)</film_or_detector_model>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>12629</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">53.62</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>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                        </software>
                    </software_list>
                    <type>PHASE FLIPPING AND AMPLITUDE CORRECTION</type>
                </ctf_correction>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.4</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>123270</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
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        <label>::::EMDATABANK.org::::EMD-47487::::</label>
        <annotation_details>structure of pertussis toxin in complex with neutralizing Fab PERT-169 and PERT-203</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
            </modelling>
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        <half_map_list>
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                    <col>600</col>
                    <row>600</row>
                    <sec>600</sec>
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                    <row>0</row>
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                    <y>600</y>
                    <z>600</z>
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                <label>::::EMDATABANK.org::::EMD-47487::::</label>
                <annotation_details>Half Map A</annotation_details>
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                    <c units="Å">503.99997</c>
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                    <beta units="deg">90.0</beta>
                    <gamma units="deg">90.0</gamma>
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                    <fast>X</fast>
                    <medium>Y</medium>
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                    <y units="Å">0.84</y>
                    <z units="Å">0.84</z>
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                <label>::::EMDATABANK.org::::EMD-47487::::</label>
                <annotation_details>Half Map B</annotation_details>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
