<?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-8711">
    <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>2017-04-26</deposition>
            <header_release>2017-08-09</header_release>
            <map_release>2017-10-18</map_release>
            <update>2024-03-13</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>Welch Foundation</funding_body>
                <code>A-1863</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>P41GM103832</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>U24GM116787</code>
                <country>United States</country>
            </grant_reference>
            <grant_reference>
                <funding_body>Public Health Service</funding_body>
                <code>GM27099</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>Phage Qbeta in complex with MurA</title>
        <authors_list>
            <author>Cui Z</author>
            <author>Zhang J</author>
        </authors_list>
        <keywords>Qbeta, ssRNA, phage, virus, VIRUS-TRANSFERASE complex</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Cui Z</author>
                    <author order="2">Gorzelnik KV</author>
                    <author order="3">Chang JY</author>
                    <author order="4">Langlais C</author>
                    <author order="5">Jakana J</author>
                    <author order="6">Young R</author>
                    <author order="7">Zhang J</author>
                    <title>Structures of Q beta virions, virus-like particles, and the Q beta-MurA complex reveal internal coat proteins and the mechanism of host lysis.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>114</volume>
                    <first_page>11697</first_page>
                    <last_page>11702</last_page>
                    <year>2017</year>
                    <external_references type="PUBMED">29078304</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1707102114</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-8710</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-8709</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-8708</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>5vm7</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Enterobacteria phage Qbeta virion with MurA</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Enterobacteria phage Qbeta virion with MurA</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
            </complex_supramolecule>
            <virus_supramolecule supramolecule_id="2">
                <name>Enterobacteria phage Qbeta</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <sci_species_name ncbi="39803">Enterobacteria phage Qbeta</sci_species_name>
                <virus_type>VIRION</virus_type>
                <virus_isolate>SPECIES</virus_isolate>
                <virus_enveloped>false</virus_enveloped>
                <virus_empty>false</virus_empty>
            </virus_supramolecule>
            <complex_supramolecule supramolecule_id="3">
                <name>UDP-N-acetylglucosamine 1-carboxyvinyltransferase</name>
                <parent>1</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="331111">Escherichia coli O139:H28 (strain E24377A / ETEC)</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Maturation protein A2</name>
                <natural_source database="NCBI">
                    <organism ncbi="39803">Escherichia phage Qbeta</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.048613078</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MPKLPRGLRFGADNEILNDFQELWFPDLFIESSDTHPWYTLKGRVLNAHLDDRLPNVGGRQVRRTPHRVTVPIASSGLRP
VTTVQYDPAALSFLLNARVDWDFGNGDSANLVINDFLFRTFAPKEFDFSNSLVPRYTQAFSAFNAKYGTMIGEGLETIKY
LGLLLRRLREGYRAVKRGDLRALRRVIQSYHNGKWKPATAGNLWLEFRYGLMPLFYDIRDVMLDWQNRHDKIQRLLRFSV
GHGEDYVVEFDNLYPAVAYFKLKGEITLERRHRHGISYANREGYAVFDNGSLRPVSDWKELATAFINPHEVAWELTPYSF
VVDWFLNVGDILAQQGQLYHNIDIVDGFDRRDIRLKSFTIKGERNGRPVNVSASLSAVDLFYSRLHTSNLPFATLDLDTT
FSSFKHVLDSIFLLTQRVKR</string>
                    <external_references type="UNIPROTKB">Q8LTE2</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>UDP-N-acetylglucosamine 1-carboxyvinyltransferase</name>
                <natural_source database="NCBI">
                    <organism ncbi="331111">Escherichia coli O139:H28 (strain E24377A / ETEC)</organism>
                    <strain>E24377A / ETEC</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.04487154299999999</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MDKFRVQGPTKLQGEVTISGAKNAALPILFAALLAEEPVEIQNVPKLKDVDTSMKLLSQLGAKVERNGSVHIDARDVNVF
CAPYDLVKTMRASIWALGPLVARFGQGQVSLPGGCTIGARPVDLHISGLEQLGATIKLEEGYVKASVDGRLKGAHIVMDK
VSVGATVTIMCAATLAEGTTIIENAAREPEIVDTANFLITLGAKISGQGTDRIVIEGVERLGGGVYRVLPDRIETGTFLV
AAAISRGKIICRNAQPDTLDAVLAKLRDAGADIEVGEDWISLDMHGKRPKAVNVRTAPHPAFPTDMQAQFTLLNLVAEGT
GFITETVFENRFMHVPELSRMGAHAEIESNTVICHGVEKLSGAQVMATDLRASASLVLAGCIAEGTTVVDRIYHIDRGYE
RIEDKLRALGANIERVKGE</string>
                    <external_references type="UNIPROTKB">A7ZS86</external_references>
                </sequence>
                <ec_number>2.5.1.7</ec_number>
            </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>7.0</ph>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">60</time>
                        </pretreatment>
                    </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 III</instrument>
                        <details>Blotted for 6s, Plunged into liquid ethane (FEI VITROBOT MARK III). </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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_magnification>30000.0</nominal_magnification>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <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_exposure_time units="s">0.2</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.0</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <image_recording_list>
                        <image_recording image_recording_id="2">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>SUPER-RESOLUTION</detector_mode>
                            <average_exposure_time units="s">0.2</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.1</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="EMDB MAP">
                    <emdb_id>EMD-8254</emdb_id>
                </startup_model>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">5.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                            <version>1.4</version>
                        </software>
                    </software_list>
                    <number_images_used>25597</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>PROJECTION MATCHING</type>
                    <projection_matching_processing/>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="131073">
        <file>emd_8711.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>320</col>
            <row>320</row>
            <sec>320</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>320</x>
            <y>320</y>
            <z>320</z>
        </spacing>
        <cell>
            <a units="Å">400.0</a>
            <b units="Å">400.0</b>
            <c units="Å">400.0</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>-0.027086757</minimum>
            <maximum>0.05751116</maximum>
            <average>0.00084872125</average>
            <std>0.004180419</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.25</x>
            <y units="Å">1.25</y>
            <z units="Å">1.25</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.012</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::D_1000227375::::</label>
        <annotation_details>Enterobacteria phage Qbeta virion with MurA</annotation_details>
    </map>
    <interpretation>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="131073">
                <file>emd_8711_additional_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>320</col>
                    <row>320</row>
                    <sec>320</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>320</x>
                    <y>320</y>
                    <z>320</z>
                </spacing>
                <cell>
                    <a units="Å">400.0</a>
                    <b units="Å">400.0</b>
                    <c units="Å">400.0</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>-0.0119275935</minimum>
                    <maximum>0.03873485</maximum>
                    <average>0.0010349842</average>
                    <std>0.0038936497</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.25</x>
                    <y units="Å">1.25</y>
                    <z units="Å">1.25</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::D_1000227375::::</label>
                <annotation_details>Enterobacteria phage Qbeta virion with MurA, additional map</annotation_details>
            </additional_map>
        </additional_map_list>
    </interpretation>
</emd>
