<?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-0359">
    <admin>
        <current_status>
            <date>2024-03-20</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-11-27</deposition>
            <header_release>2019-02-20</header_release>
            <map_release>2019-03-06</map_release>
            <update>2024-03-20</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)</funding_body>
                <code>1S10RR23057</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase in complex with ssDNA, dTTP, AC dinucleotide and CTP (form I)</title>
        <authors_list>
            <author>Gao Y</author>
            <author>Cui Y</author>
        </authors_list>
        <keywords>helicase, ATPase, hexamer, DNA replication, HYDROLASE, TRANSFERASE-DNA complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author ORCID="0000-0002-4037-0431" order="1">Gao Y</author>
                    <author ORCID="0000-0002-8909-6576" order="2">Cui Y</author>
                    <author ORCID="0000-0002-9324-1756" order="3">Fox T</author>
                    <author ORCID="0000-0001-7181-4261" order="4">Lin S</author>
                    <author ORCID="0000-0002-7466-0090" order="5">Wang H</author>
                    <author order="6">de Val N</author>
                    <author ORCID="0000-0002-8373-4717" order="7">Zhou ZH</author>
                    <author ORCID="0000-0002-3591-2195" order="8">Yang W</author>
                    <title>Structures and operating principles of the replisome.</title>
                    <journal_abbreviation>Science</journal_abbreviation>
                    <country>US</country>
                    <volume>363</volume>
                    <year>2019</year>
                    <external_references type="PUBMED">30679383</external_references>
                    <external_references type="DOI">doi:10.1126/science.aav7003</external_references>
                    <external_references type="ISSN">1095-9203</external_references>
                    <external_references type="CSD">0038</external_references>
                    <external_references type="ASTM">SCIEAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-0357</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0362</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0363</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0364</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-0365</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6n7n</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex I</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex I</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="10760">Enterobacteria phage T7</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>DNA primase/helicase</name>
                <natural_source database="NCBI">
                    <organism ncbi="10760">Enterobacteria phage T7</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.06273443</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MDNSHDSDSVFLYHIPCDNCGSSDGNSLFSDGHTFCYVCEKWTAGNEDTKERASKRKPSGGKPMTYNVWNFGESNGRYSA
LTARGISKETCQKAGYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIVVTEGEI
DMLTVMELQDCKYPVVSLGHGASAAKKTCAANYEYFDQFEQIILMFDMDEAGRKAVEEAAQVLPAGKVRVAVLPCKDANE
CHLNGHDREIMEQVWNAGPWIPDGVVSALSLRERIREHLSSEESVGLLFSGCTGINDKTLGARGGEVIMVTSGSGMGKST
FVRQQALQWGTAMGKKVGLAMLQESVEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEA
ETDRLLAKLAYMRSGLGCDVIILDHISIVVSASGESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAHEEGRP
VSITDLRGSGALRQLSDTIIALERNQQGDMPNLVLVRILKCRFTGDTGIAGYMEYNKETGWLEPSSYSGEEESHSESTDW
SNDTDF</string>
                    <external_references type="UNIPROTKB">P03692</external_references>
                </sequence>
                <ec_number>2.7.7.-</ec_number>
            </protein_or_peptide>
            <dna macromolecule_id="2">
                <name>DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')</name>
                <natural_source database="NCBI">
                    <organism ncbi="10760">Enterobacteria phage T7</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.004517935</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <sequence>
                    <string>(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)</string>
                </sequence>
                <classification>DNA</classification>
            </dna>
            <ligand macromolecule_id="3">
                <name>THYMIDINE-5'-TRIPHOSPHATE</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000482168</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <formula>TTP</formula>
            </ligand>
            <ligand macromolecule_id="4">
                <name>MAGNESIUM ION</name>
                <molecular_weight>
                    <theoretical units="MDa">2.4305e-05</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <formula>MG</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">
                    <buffer>
                        <ph>7.5</ph>
                        <component>
                            <concentration units="mM">50.0</concentration>
                            <name>Tris</name>
                        </component>
                        <component>
                            <concentration units="mM">150.0</concentration>
                            <formula>KCl</formula>
                            <name>potassium chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">3.0</concentration>
                            <name>DTT</name>
                        </component>
                    </buffer>
                    <grid>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">295</chamber_temperature>
                        <instrument>FEI VITROBOT MARK I</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>
                    <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>
                            <average_electron_dose_per_image units="e/Å^2">72.0</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="PDB ENTRY">
                    <pdb_model>
                        <pdb_id>1E0J</pdb_id>
                    </pdb_model>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.5</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>61143</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="67109">
        <file>emd_0359.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>256</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>256</z>
        </spacing>
        <cell>
            <a units="Å">273.92</a>
            <b units="Å">273.92</b>
            <c units="Å">273.92</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>-0.16553569</minimum>
            <maximum>0.22825494</maximum>
            <average>0.0005795946</average>
            <std>0.005860564</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>0.026</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-0359::::</label>
        <annotation_details>Bacteriophage T7 gene product 4 (gp4) helicase primase DNA complex I</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1E0J</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
