<?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_2/emdb.xsd" version="3.0.9.2" emdb_id="EMD-7046">
    <admin>
        <current_status>
            <date>2024-03-13</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2017-09-25</deposition>
            <header_release>2017-10-18</header_release>
            <map_release>2019-03-20</map_release>
            <update>2024-03-13</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>NIH R37AI32524</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>UEFISCDI</funding_body>
                <code>PN-III-ID-PCE-2016-0650</code>
                <country>Romania</country>
            </grant_reference>
        </grant_support>
        <title>BbRAGL-3'TIR synaptic complex with nicked DNA refined with C2 symmetry</title>
        <authors_list>
            <author>Zhang Y</author>
            <author>Cheng TC</author>
        </authors_list>
        <keywords>DNA transposase, DNA cut and paste transposition, DDE family RNase H fold DNA transposase, RECOMBINATION</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Zhang Y</author>
                    <author order="2">Cheng TC</author>
                    <author order="3">Huang G</author>
                    <author order="4">Lu Q</author>
                    <author order="5">Surleac MD</author>
                    <author order="6">Mandell JD</author>
                    <author order="7">Pontarotti P</author>
                    <author order="8">Petrescu AJ</author>
                    <author order="9">Xu A</author>
                    <author order="10">Xiong Y</author>
                    <author order="11">Schatz DG</author>
                    <title>Transposon molecular domestication and the evolution of the RAG recombinase.</title>
                    <journal_abbreviation>Nature</journal_abbreviation>
                    <country>UK</country>
                    <volume>569</volume>
                    <first_page>79</first_page>
                    <last_page>84</last_page>
                    <year>2019</year>
                    <external_references type="PUBMED">30971819</external_references>
                    <external_references type="DOI">doi:10.1038/s41586-019-1093-7</external_references>
                    <external_references type="ISSN">1476-4687</external_references>
                    <external_references type="CSD">0006</external_references>
                    <external_references type="ASTM">NATUAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-7078</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-7077</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6b40</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>BbRAGL-31TIR synaptic complex with nicked DNA</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>BbRAGL-31TIR synaptic complex with nicked DNA</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_list>
                <natural_source database="NCBI">
                    <organism ncbi="7741">Branchiostoma belcheri</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.35</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>RAG1L,RAG1L</name>
                <natural_source database="NCBI">
                    <organism ncbi="7741">Branchiostoma belcheri</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.07444013299999999</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>ESLQRKRLCKARLYDVTRHHVKHKRLKPLIEHIDEYCNEKDENKGDVLFFLLRSHLYDTGNRSMAEQIDTLWHGESLSCM
TPEECLGMRLDMLMTKNQYSKEYNILKERGFSTLCPPKQLDAIEKTLMPGTARYSIEGMDYSEHYFHSPVKMTGDLEVHS
GETLEPDSVTMDFHEYVPDFPCPNTKGVRFPYAHAVAKTLEELEDEIVNGLKKLGRDPNDPTLVIHTICKDGADGMGDVS
VHKEKSDHLLPDKALRFSFCVLRCSVMHKDTEVTIYEDPNPNSVRSNRPVLECIGDENDDGTVAVCVGPIECQRLLMKDK
IMRVHMSDGTQRAHYLTFFNSMVDEKWDRAHGGLAGAGSKYLCTLCEAVRDEALEKAGSYKITRTLKKIEVTASKMKYES
QEKDTFGVKGYPLLTTEPWERGIDATHTDINMGNYFKSLIVREMAQVHSWAKTANVKKQIVDAESKLDKHLKESLGLNPT
LMMAGNYARELFKAEHADKLVALVDKPDRKSALVEVLAKFRQLRKVYRANWPLNDMSDEVRQYKAKAVEMANDLKTHFPY
APCTNYLHKVIEHVQELIEHPSGVGSVGALSSEGNEAGNKLFRQLRLGHARKGNTYNGLRDVLCTHWLYTSKTLRDKAA
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)</string>
                    <external_references type="UNIPROTKB">A0A185KID9</external_references>
                </sequence>
            </protein_or_peptide>
            <dna macromolecule_id="2">
                <name>31TIR intact strand</name>
                <natural_source database="NCBI">
                    <organism ncbi="7741">Branchiostoma belcheri</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.019218312</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <sequence>
                    <string>(DC)(DA)(DA)(DG)(DA)(DT)(DG)(DG)(DC)(DG)(DA)(DC)(DC)(DA)(DG)(DA)(DC)(DA)(DC)(DT)
(DG)(DC)(DT)(DG)(DG)(DG)(DT)(DA)(DT)(DA)(DG)(DC)(DG)(DT)(DA)(DA)(DG)(DT)(DA)(DT)
(DC)(DA)(DT)(DA)(DG)(DT)(DG)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DC)(DC)(DA)
(DA)(DG)</string>
                </sequence>
                <classification>DNA</classification>
            </dna>
            <dna macromolecule_id="3">
                <name>31TIR pre-nicked strand of signal DNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="7741">Branchiostoma belcheri</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.014357205999999999</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <sequence>
                    <string>(DC)(DA)(DC)(DT)(DA)(DT)(DG)(DA)(DT)(DA)(DC)(DT)(DT)(DA)(DC)(DG)(DC)(DT)(DA)(DT)
(DA)(DC)(DC)(DC)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DT)(DC)(DT)(DG)(DG)(DT)(DC)(DG)(DC)
(DC)(DA)(DT)(DC)(DT)(DT)(DG)</string>
                </sequence>
                <classification>DNA</classification>
            </dna>
            <dna macromolecule_id="4">
                <name>31TIR pre-nicked strand of flanking DNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="7741">Branchiostoma belcheri</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.004601970999999999</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <sequence>
                    <string>(DC)(DT)(DT)(DG)(DG)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)</string>
                </sequence>
                <classification>DNA</classification>
            </dna>
            <protein_or_peptide macromolecule_id="5">
                <name>RAG2L</name>
                <natural_source database="NCBI">
                    <organism ncbi="7741">Branchiostoma belcheri</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.039509254</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>MSSGPIFSSLVTDSSRSSRKKSDSALGTEFTVVCDRVPLRDPSPTVQRFLCFVFDNGSGAMSTLPIDVGGEGISLSDMKE
VKAMPHIASGCTAVWGPPLPPKPGKDTKQVILWGGLDKRRWCCSNDLTQVDITITPKTTTAKVSILPADKQDGVPSPRTG
HTLVAISSLQAILFGGLELASRHARLGTCAQSCKDGYFYLLDMTTLRWNKLPLPPLVPRAYHSSTWVPASSTMVIVGGIT
YSGHCPSERLSVSDVVCLKISDTSQYTLTEIHMEGVRDSYVSSSSASALCDDRFVLYGGYHHDKSGLHPPEPSRDLYVMN
LQTKKAVVHHAPTRMASAGHTCLRLIDNSVVMIGGTCKSVNCCTNL</string>
                    <external_references type="UNIPROTKB">A0A185KIE0</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="6">
                <name>CALCIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">4.0078e-05</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>CA</formula>
            </ligand>
            <ligand macromolecule_id="7">
                <name>ZINC ION</name>
                <molecular_weight>
                    <theoretical units="MDa">6.5409e-05</theoretical>
                </molecular_weight>
                <number_of_copies>2</number_of_copies>
                <formula>ZN</formula>
            </ligand>
        </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">0.4</concentration>
                    <buffer>
                        <ph>7.6</ph>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3 4C</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">45</time>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">283</chamber_temperature>
                        <instrument>FEI VITROBOT MARK III</instrument>
                    </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">0.01</nominal_cs>
                    <nominal_defocus_min units="µm">1.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.5</nominal_defocus_max>
                    <nominal_magnification>81000.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <lower_energy_threshold units="eV">0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20</upper_energy_threshold>
                        </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>SUPER-RESOLUTION</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">7676</width>
                                    <height units="pixel">7420</height>
                                </dimensions>
                                <frames_per_image>3-40</frames_per_image>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>4429</number_real_images>
                            <average_exposure_time units="s">10.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">54.0</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>496221</number_selected>
                </particle_selection>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-6488</emdb_id>
                </startup_model>
                <final_reconstruction>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <algorithm>BACK PROJECTION</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">4.3</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                    <number_images_used>350143</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>2.1</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="23329">
        <file>emd_7046.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>180</col>
            <row>180</row>
            <sec>180</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="Å">243.0</a>
            <b units="Å">243.0</b>
            <c units="Å">243.0</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>-0.117407314</minimum>
            <maximum>0.22704715</maximum>
            <average>0.0014140488</average>
            <std>0.010697988</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.35</x>
            <y units="Å">1.35</y>
            <z units="Å">1.35</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.07</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-7046::::</label>
        <annotation_details>BbRAGL-31TIR synaptic complex with nicked DNA refined with C2 symmetry</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
