<?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_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-0844">
    <admin>
        <current_status>
            <date>2024-10-23</date>
            <code>REL</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>PDBj</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2019-11-01</deposition>
            <header_release>2021-03-31</header_release>
            <map_release>2021-03-31</map_release>
            <update>2024-10-23</update>
        </key_dates>
        <title>Signal substraction of TcdB1-TccC2 and part of TcdA1</title>
        <authors_list>
            <author>Yan ZF</author>
            <author>Yang GW</author>
        </authors_list>
        <keywords>protein transportation, TcdA1, TcdB1, TccC2, TOXIN-PROTEIN TRANSPORT complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Yan ZF</author>
                    <author order="2">Zhang N</author>
                    <author order="3">Yang GW</author>
                    <title>Signal substraction of TcdB1-TccC2 and part of TcdA1</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>6l7i</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Toxin complex TcdA1-TcdB1-TccC2</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Toxin complex TcdA1-TcdB1-TccC2</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_list>
                <natural_source database="NCBI">
                    <organism ncbi="29488">Photorhabdus luminescens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>TcdA1</name>
                <natural_source database="NCBI">
                    <organism ncbi="29488">Photorhabdus luminescens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.020255886999999997</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>RALEVERTVSLAEVYAGLPKDNGPFSLAQEIDKLVSQGSGSAGSGNNNLAFGAGTDTKTSLQASVSFADLKIREDYPASL
GKIRRIKQISVTLPALLGPYQDVQAILSYGDKAGLANGCEALAVSHGMNDSGQFQLDFNDGKFLPFEGIAIDQGTLTLSF
PNASMPEKGKQATMLKTLNDIILHIRYTIK</string>
                    <external_references type="UNIPROTKB">Q9RN43</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>TcdB1</name>
                <natural_source database="NCBI">
                    <organism ncbi="29488">Photorhabdus luminescens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.165296453</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MQNSQTFSVTELSLPKGGGAITGMGEALTPAGPDGMAALSLPLPISAGRGYAPSLTLNYNSGTGNSPFGLGWDCGVMAIR
RRTSTGVPNYDETDTFLGPEGEVLVVALNEAGQADIRSESSLQGINLGATFTVTCYRSRLESHFNRLEYWQPQTTGATDF
WLIYSPDGQVHLLGKNPQARISNPLNVNQTAQWLLEASISSHSEQIYYQYRAEDEAGCETDELAAHPSATVQRYLQTVHY
GNLTASDVFPTLNGDDPLKSGWMFCLVFDYGERKNSLSEMPLFKATGNWLCRKDRFSRYEYGFELRTRRLCRQILMFHRL
QTLSGQAKGDDEPALVSRLILDYDENAMVSTLVSVRRVGHEDNNTVTALPPLELAYQPFEPEQTALWQSMDVLANFNTIQ
RWQLLDLKGEGVPGILYQDRNGWWYRSAQRQAGEEMNAVTWGKMQLLPITPAVQDNASLMDINGDGQLDWVITGPGLRGY
HSQHPDGSWTRFTPLHALPIEYSHPRAQLADLMGAGLSDLVLIGPKSVRLYVNNRDGFTEGRDVVQSGDITLPLPGADAR
KLVAFSDVLGSGQAHLVEVSATQVTCWPNLGHGRFGQPIVLPGFSQSAASFNPDRVHLADLDGSGPADLIYVHADRLDIF
SNESGNGFAKPFTLSFPDGLRFDDTCQLQVADVQGLGVVSLILSVPHMAPHHWRCDLTNAKPWLLSETNNNMGANHTLHY
RSSVQFWLDEKAAALATGQTPVCYLPFPVHTLWQTETEDEISGNKLVTTLRYAHGAWDGREREFRGFGYVEQTDSHQLAQ
GNAPERTPPALTKSWYATGLPAVDNALSAGYWRGDKQAFAGFTPRFTLWKEGKDVPLTPEDDHNLYWLNRALKGQPLRSE
LYGLDGSAQQQIPYTVTESRPQVRQLQDGATVSPVLWASVVESRSYHYERIISDPQCNQDITLSSDLFGQPLKQVSVQYP
RRNKPTTNPYPDTLPDTLFASSYDDQQQLLRLTCRQSSWHHLIGNELRVLGLPDGTRSDAFTYDAKQVPVDGLNLETLCA
ENSLIADDKPREYLNQQRTFYTDGKNQTPLKTPTRQALIAFTETAVLTESLLSAFDGGITPDELPGILTQAGYQQEPYLF
PRTGENKVWVARQGYTDYGTEAQFWRPVAQRNSLLTGKMTLKWDTHYCVITQTQDAAGLTVSANYDWRFLTPTQLTDIND
NVHLITLDALGRPVTQRFWGIESGVATGYSSSEEKPFSPPNDIDTAINLTGPLPVAQCLVYAPDSWMPLFSQETFNTLTQ
EEQETLRDSRIITEDWRICALTRRRWLQSQKISTPLVKLLTNSIGLPPHNLTLTTDRYDRDSEQQIRQQVAFSDGFGRLL
QASVRHEAGEAWQRNQDGSLVTKVENTKTRWAVTGRTEYDNKGQTIRTYQPYFLNDWRYVSDDSARKEAYADTHIYDPIG
REIRVITAKGWLRQSQYFPWFTVSEDENDTAADALV</string>
                    <external_references type="UNIPROTKB">Q93EP6</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>TccC2</name>
                <natural_source database="NCBI">
                    <organism ncbi="29488">Photorhabdus luminescens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.074759125</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MSSYNSAIDQKTPSIKVLDNRKLNVRTLEYLRTQADENSDELITFYEFNIPGFQVKSTDPRKNKNQSGPNFIRVFNLAGQ
VLREESVDAGRTITLNDIESRPVLIINATGVRQNHRYEDNTLPGRLLAITEQVQAGEKTTERLIWAGNTPQEKDYNLAGQ
CVRHYDTAGLTQLNSLSLAGVVLSQSQQLLVDDKNADWTGEDQSLWQQKLSSDVYTTQNKADATGALLTQTDAKGNIQRL
AYDVAGQLKGCWLTLKGQAEQVIIKSLTYSAAGQKLREEHGNGVITEYSYEPETQRLIGIATRRPSDAKVLQDLRYQYDP
VGNVINIRNDAEATRFWRNQKVVPENSYTYDSLYQLISATGREMANIGQQNNQLPSPALPSDNNTYTNYTRSYSYDHSGN
LTQIRHSSPATQNNYTVAITLSNRSNRGVLSTLTTDPNQVDTLFDAGGHQTSLLPGQTLIWTPRGELKQVNNGPGNEWYR
YDSNGMRQLKVSEQPTQNTTQQQRVIYLPGLELRTTQSNATTTEELHVITLGEAGRAQVRVLHWESGKPEDVNNNQLRYS
YDNLIGSSQLELDNQGQIISEEEYYPFGGTALWAANSQTEASYKTIRYSGKERDATGLYYYGYRYYQPWAGRWLSADPAG
TIDGLNLYRMVRNNPVSLQDENGL</string>
                    <external_references type="UNIPROTKB">Q93EP1</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="4">
                <name>TccC2</name>
                <natural_source database="NCBI">
                    <organism ncbi="29488">Photorhabdus luminescens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.001905087</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>APEKGKYTKEVNFFDE</string>
                    <external_references type="UNIPROTKB">Q93EP1</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">
                    <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>FEI/PHILIPS CM300FEG/HE</microscope>
                    <illumination_mode>SPOT SCAN</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <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>
                <startup_model type_of_model="OTHER"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">2.9</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>124828</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>
    <map format="CCP4" size_kbytes="219489">
        <file>emd_0844.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>380</col>
            <row>380</row>
            <sec>380</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>380</x>
            <y>380</y>
            <z>380</z>
        </spacing>
        <cell>
            <a units="Å">508.44003</a>
            <b units="Å">508.44003</b>
            <c units="Å">508.44003</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>-1.1598004</minimum>
            <maximum>0.69353884</maximum>
            <average>0.00009251639</average>
            <std>0.0062564625</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.338</x>
            <y units="Å">1.338</y>
            <z units="Å">1.338</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.005</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0844::::</label>
        <annotation_details>B1C1 and part of A1</annotation_details>
    </map>
</emd>
