<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_9/emdb.xsd" emdb_id="EMD-11525" version="3.0.1.9">
    <admin>
        <current_status>
            <date>2020-09-02</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2020-07-29</deposition>
            <header_release>2020-09-02</header_release>
            <map_release>2020-09-02</map_release>
            <update>2020-09-02</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>European Research Council (ERC)</funding_body>
                <code>615984</code>
                <country>Germany</country>
            </grant_reference>
        </grant_support>
        <title>Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1A)' arrangement</title>
        <authors_list>
            <author>Quentin D</author>
            <author>Antoni C</author>
            <author>Gatsogiannis C</author>
            <author>Raunser S</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Antoni C</author>
                    <author order="2">Quentin D</author>
                    <author order="3">Lang AE</author>
                    <author order="4">Aktories K</author>
                    <author order="5">Gatsogiannis C</author>
                    <author order="6">Raunser S</author>
                    <title>Cryo-EM structure of the fully-loaded asymmetric anthrax lethal toxin in its heptameric pre-pore state.</title>
                    <journal_abbreviation>Plos Pathog.</journal_abbreviation>
                    <country>US</country>
                    <volume>16</volume>
                    <first_page>e1008530</first_page>
                    <last_page>e1008530</last_page>
                    <year>2020</year>
                    <external_references type="PUBMED">32810181</external_references>
                    <external_references type="DOI">doi:10.1371/journal.ppat.1008530</external_references>
                    <external_references type="ISSN">1553-7374</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-11525</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1A)' arrangement</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Fully-loaded anthrax lethal toxin in its heptameric pre-pore state and PA7LF(2+1A)' arrangement</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Three LF molecules crown the heptameric PA ring. The LFs form a continuous chain of head-to-tail interactions. In the PA7LF(2+1A)' arrangement, the third LF binds with its N-terminal domain to the C-terminal region of the 2nd LF. In addition, two LFs likely interact with each other via their C-terminal regions close to the central axis of the complex.</details>
                <molecular_weight>
                    <theoretical units="MDa">0.093</theoretical>
                </molecular_weight>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="2">
                <name>Protective antigen</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>The trypsin-activated 63 kDa fragments assemble into a hepatameric pre-pore</details>
                <natural_source database="NCBI">
                    <organism ncbi="1392">Bacillus anthracis</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21 (DE3)</recombinant_strain>
                </recombinant_expression>
            </complex_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>Lethal factor</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Three LF molecules crown the heptameric PA ring. The LFs form a continuous chain of head-to-tail interactions. In the PA7LF(2+1A) arrangement, the third LF binds with its N-terminal domain to the C-terminus of the 2nd LF. In addition, two LFs likely interact with each other via their C-terminal regions close to the central axis of the complex.</details>
                <natural_source database="NCBI">
                    <organism ncbi="1392">Bacillus anthracis</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="1392">Bacillus anthracis</recombinant_organism>
                </recombinant_expression>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Protective antigen</name>
                <natural_source database="NCBI">
                    <organism ncbi="1392">Bacillus anthracis</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MGHHHHHHHHHHSSGHIDDDDKHMEVKQENRLLNESESSSQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSENQYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIKIQYQRENPTEKGLDFKLYWTDSQNKKEVISSDNLQLPELKQKSSNSRKKRSTSAGPTVPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTSRTHTSEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYVNTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGADESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEIG</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Lethal factor</name>
                <natural_source database="NCBI">
                    <organism ncbi="1392">Bacillus anthracis</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="1392">Bacillus anthracis</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MNIKKEFIKVISMSCLVTAITLSGPVFIPLVQGAGGHGDVGMHVKEKEKNKDENKRKDEE
RNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGD
ITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALNV
YYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLE
QNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFNEQEINLSLEELKDQRMLAR
YEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSS
DFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYD
INQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLT
ATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSP
DTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNIN
QEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNG
RFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHE
FGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHST
DHAERLKVQKNAPKTFQFINDQIKFIINS
</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">
                    <concentration units="mg/mL">0.06</concentration>
                    <buffer>
                        <ph>8.5</ph>
                        <component>
                            <concentration units="mM">20.0</concentration>
                            <formula>Tris-HCl</formula>
                            <name>Tris hydrochloride</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>NaCl</formula>
                            <name>sodium chloride</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>CONTINUOUS</film_topology>
                            <film_thickness units="nm">2.0</film_thickness>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">286</chamber_temperature>
                        <instrument>GATAN CRYOPLUNGE 3</instrument>
                        <details>4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting.. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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_cs units="mm">2.7</nominal_cs>
                    <calibrated_defocus_min units="µm">1.2</calibrated_defocus_min>
                    <calibrated_defocus_max units="µm">2.6</calibrated_defocus_max>
                    <nominal_magnification>130000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <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 K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details/>
                            <number_real_images>5238</number_real_images>
                            <average_exposure_time units="s">15.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">74.4</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>382000</number_selected>
                </particle_selection>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>SPHIRE</name>
                        </software>
                    </software_list>
                </ctf_correction>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>1TZO</pdb_id>
                    </pdb_model>
                    <details>The corresponding 3D class of the 3D classification step served as initial model for the refinement</details>
                </startup_model>
                <startup_model type_of_model="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>1J7N</pdb_id>
                    </pdb_model>
                    <details>The corresponding 3D class of the 3D classification step served as initial model for the refinement</details>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C1</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">4.3</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPHIRE</name>
                        </software>
                    </software_list>
                    <number_images_used>30000</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>SPHIRE</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
                <final_three_d_classification>
                    <software_list>
                        <software>
                            <name>SPHIRE</name>
                        </software>
                    </software_list>
                </final_three_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="151733">
        <file>emd_11525.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>336</col>
            <row>336</row>
            <sec>336</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>336</x>
            <y>336</y>
            <z>336</z>
        </spacing>
        <cell>
            <a units="Å">359.52002</a>
            <b units="Å">359.52002</b>
            <c units="Å">359.52002</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>-0.66913307</minimum>
            <maximum>1.0001136</maximum>
            <average>0.0012471832</average>
            <std>0.023108173</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.07</x>
            <y units="Å">1.07</y>
            <z units="Å">1.07</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.07</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-11525::::</label>
        <annotation_details>PA7LF(2 1A)'</annotation_details>
    </map>
</emd>
