<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2993" version="3.0.1.1" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_1/emdb_relaxed.xsd">
   <admin>
      <current_status>
         <code>REL</code>
         <processing_site>PDBe</processing_site>
      </current_status>
      <sites>
         <deposition>PDBe</deposition>
         <last_processing>PDBe</last_processing>
      </sites>
      <key_dates>
         <deposition>2015-05-03</deposition>
         <header_release>2015-05-27</header_release>
         <map_release>2015-06-03</map_release>
         <update>2015-06-17</update>
      </key_dates>
      <title>Structural rearrangements in the phage head-to-tail interface during assembly and infection</title>
      <authors_list>
         <author>Chaban Y</author>
         <author>Lurz R</author>
         <author>Brasiles S</author>
         <author>Cornilleau C</author>
         <author>Karreman M</author>
         <author>Zinn-Justin S</author>
         <author>Tavares P</author>
         <author>Orlova EV</author>
      </authors_list>
      <keywords>viral infection, tailed bacteriophage, Siphoviridae, SPP1, viral assembly, head-to-tail interface, DNA gatekeeper, allosteric mechanism, concerted reorganisation, diaphragm gating</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Chaban Y</author>
               <author order="2">Lurz R</author>
               <author order="3">Brasiles S</author>
               <author order="4">Cornilleau C</author>
               <author order="5">Karreman M</author>
               <author order="6">Zinn-Justin S</author>
               <author order="7">Tavares P</author>
               <author order="8">Orlova EV</author>
               <title>Structural rearrangements in the phage head-to-tail interface during assembly and infection.</title>
               <journal>PROC.NAT.ACAD.SCI.USA</journal>
               <volume>112</volume>
               <first_page>7009</first_page>
               <last_page>7014</last_page>
               <year>2015</year>
               <external_references type="PUBMED">25991862</external_references>
               <external_references type="DOI">doi:10.1073/pnas.1504039112</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>5a20</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>Bacteriophage SPP1 head-to-tail interface</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Bacteriophage SPP1 head-to-tail interface</name>
            <details>The sample was monodisperse</details>
            <oligomeric_state>cyclical dodecamers and hexamers</oligomeric_state>
            <number_unique_components>5</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">1.2</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="gp6">Bacteriophage SPP1 portal protein gp6</name>
            <natural_source database="NCBI">
               <organism ncbi="10724">Bacillus phage SPP1</organism>
               <strain>Bacillus phage SPP1</strain>
               <synonym_organism>bacteriophage SPP1</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.0572</experimental>
               <theoretical units="MDa">0.0573225</theoretical>
            </molecular_weight>
            <number_of_copies>12</number_of_copies>
            <oligomeric_state>cyclical dodecamer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P54309</external_references>
               <external_references type="INTERPRO">IPR006428</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="gp15">head completion protein gp15</name>
            <natural_source database="NCBI">
               <organism ncbi="10724">Bacillus phage SPP1</organism>
               <strain>Bacillus phage SPP1</strain>
               <synonym_organism>bacteriophage SPP1</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.0116</experimental>
               <theoretical units="MDa">0.0116144</theoretical>
            </molecular_weight>
            <number_of_copies>12</number_of_copies>
            <oligomeric_state>cyclical dodecamer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q38584</external_references>
               <external_references type="INTERPRO">IPR021146</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="3">
            <name synonym="gp16">head completion protein gp16</name>
            <natural_source database="NCBI">
               <organism ncbi="10724">Bacillus phage SPP1</organism>
               <strain>Bacillus phage SPP1</strain>
               <synonym_organism>bacteriophage SPP1</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.0125</experimental>
               <theoretical units="MDa">0.012542</theoretical>
            </molecular_weight>
            <number_of_copies>12</number_of_copies>
            <oligomeric_state>cyclical dodecamer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">O48446</external_references>
               <external_references type="INTERPRO">IPR008767</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="4">
            <name synonym="gp17">tail-to-head joining protein gp17</name>
            <natural_source database="NCBI">
               <organism ncbi="10724">Bacillus phage SPP1</organism>
               <strain>Bacillus phage SPP1</strain>
               <synonym_organism>bacteriophage SPP1</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.015</experimental>
               <theoretical units="MDa">0.01501</theoretical>
            </molecular_weight>
            <number_of_copies>6</number_of_copies>
            <oligomeric_state>cyclical hexamer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">O48448</external_references>
               <external_references type="INTERPRO">IPR021508</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="5">
            <name synonym="gp17.1">major tail protein gp17.1</name>
            <natural_source database="NCBI">
               <organism ncbi="10724">Bacillus phage SPP1</organism>
               <strain>Bacillus phage SPP1</strain>
               <synonym_organism>bacteriophage SPP1</synonym_organism>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.0192</experimental>
               <theoretical units="MDa">0.0191158</theoretical>
            </molecular_weight>
            <number_of_copies>6</number_of_copies>
            <oligomeric_state>cyclical hexamer</oligomeric_state>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">O48449</external_references>
               <external_references type="INTERPRO">IPR011855</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>7.5</ph>
                  <details>50 mM NaCl, 50 mM Tris-Cl, 5 mM MgCl2</details>
               </buffer>
               <grid>
                  <details>holey carbon coated Quantifoil grids (r2/2) (Quantifoil, Germany)</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <instrument>FEI VITROBOT MARK II</instrument>
                  <method>blot for 2 seconds</method>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <single_particle_microscopy microscopy_id="1">
               <microscope>FEI POLARA 300</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">2.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.9</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.6</nominal_defocus_max>
               <nominal_magnification>39000.0</nominal_magnification>
               <specimen_holder_model>OTHER</specimen_holder_model>
               <date>2008-10-09</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                     <digitization_details>
                        <scanner>PRIMESCAN</scanner>
                        <sampling_interval units="&#181;m">4</sampling_interval>
                     </digitization_details>
                     <number_real_images>200</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                     <bits_per_pixel>16.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C6</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">7.6</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>Imagic, Spider, EMAN</name>
                  </software>
               </software_list>
               <number_images_used>14000</number_images_used>
            </final_reconstruction>
            <final_two_d_classification>
               <number_classes>3500</number_classes>
            </final_two_d_classification>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="54001">
      <file>emd_2993.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>240</col>
         <row>240</row>
         <sec>240</sec>
      </dimensions>
      <origin>
         <col>-120</col>
         <row>-120</row>
         <sec>-120</sec>
      </origin>
      <spacing>
         <x>240</x>
         <y>240</y>
         <z>240</z>
      </spacing>
      <cell>
         <a units="&#8491;">276.0</a>
         <b units="&#8491;">276.0</b>
         <c units="&#8491;">276.0</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>-0.31219065</minimum>
         <maximum>0.43653822</maximum>
         <average>0.00406044</average>
         <std>0.02318234</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.15</x>
         <y units="&#8491;">1.15</y>
         <z units="&#8491;">1.15</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.06</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein.</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2993::::</details>
   </map>
   <interpretation>
      <modelling_list>
         <modelling>
            <initial_model>
               <access_code>2JES</access_code>
            </initial_model>
            <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera, VEDA (UROX), Modeller Flex-EM</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>2KBZ</access_code>
            </initial_model>
            <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera, VEDA (UROX), Modeller Flex-EM</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>2KCA</access_code>
            </initial_model>
            <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera, VEDA (UROX), Modeller Flex-EM</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
         <modelling>
            <initial_model>
               <access_code>2LFP</access_code>
            </initial_model>
            <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
            <software_list>
               <software>
                  <name>Chimera, VEDA (UROX), Modeller Flex-EM</name>
               </software>
            </software_list>
            <refinement_space>REAL</refinement_space>
         </modelling>
      </modelling_list>
   </interpretation>
</emd>