<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2331" 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>2013-03-14</deposition>
         <header_release>2013-04-10</header_release>
         <map_release>2013-06-05</map_release>
         <update>2013-07-17</update>
      </key_dates>
      <title>Negative stain reconstruction of BG505 SOSIP gp140 HIV-1 trimer in complex with PGT135 Fab</title>
      <authors_list>
         <author>Lee JH</author>
         <author>Kong L</author>
         <author>Murin CD</author>
         <author>Cupo A</author>
         <author>Moore JP</author>
         <author>Wilson IA</author>
         <author>Ward AB</author>
      </authors_list>
      <keywords>HIV, SOSIP, broadly neutralizing antibodies</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Kong L</author>
               <author order="2">Lee JH</author>
               <author order="3">Doores KJ</author>
               <author order="4">Murin CD</author>
               <author order="5">Julien JP</author>
               <author order="6">McBride R</author>
               <author order="7">Liu Y</author>
               <author order="8">Marozsan A</author>
               <author order="9">Cupo A</author>
               <author order="10">Klasse PJ</author>
               <author order="11">Hoffenberg S</author>
               <author order="12">Caulfield M</author>
               <author order="13">King CR</author>
               <author order="14">Hua Y</author>
               <author order="15">Le KM</author>
               <author order="16">Khayat R</author>
               <author order="17">Deller MC</author>
               <author order="18">Clayton T</author>
               <author order="19">Tien H</author>
               <author order="20">Feizi T</author>
               <author order="21">Sanders RW</author>
               <author order="22">Paulson JC</author>
               <author order="23">Moore JP</author>
               <author order="24">Stanfield RL</author>
               <author order="25">Burton DR</author>
               <author order="26">Ward AB</author>
               <author order="27">Wilson IA</author>
               <title>Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.</title>
               <journal>NAT.STRUCT.MOL.BIOL.</journal>
               <volume>20</volume>
               <first_page>796</first_page>
               <last_page>803</last_page>
               <year>2013</year>
               <external_references type="PUBMED">23708606</external_references>
               <external_references type="DOI">doi:10.1038/nsmb.2594</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer.</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>PGT135 Fab fragment bound to HIV-1 clade A BG505 background SOSIP gp140 trimer.</name>
            <oligomeric_state>One Fab binds one gp140 monomer</oligomeric_state>
            <number_unique_components>2</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.5</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>HIV-1 SOSIP.664 gp140</name>
            <natural_source database="NCBI">
               <organism ncbi="11676">Human immunodeficiency virus 1</organism>
               <strain>BG505</strain>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.35</theoretical>
            </molecular_weight>
            <details>co-expressed with Furin</details>
            <number_of_copies>3</number_of_copies>
            <oligomeric_state>trimer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
               <recombinant_strain>human</recombinant_strain>
               <recombinant_cell>HEK293S</recombinant_cell>
               <recombinant_plasmid>pPPI4</recombinant_plasmid>
            </recombinant_expression>
            <sequence>
               </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="bnAb PGT135">PGT135 broadly neutralizing antibody</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
               <cell>B-Cell</cell>
            </natural_source>
            <molecular_weight>
               <theoretical units="MDa">0.05</theoretical>
            </molecular_weight>
            <number_of_copies>3</number_of_copies>
            <oligomeric_state>monomer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
               <recombinant_cell>SF9</recombinant_cell>
            </recombinant_expression>
            <sequence>
               </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">0.03</concentration>
               <buffer>
                  <ph>7.4</ph>
                  <details>1x TBS</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Stained with 2% UF</details>
               </staining>
               <grid>
                  <details>400 Cu mesh grid glow discharged at 20 mA</details>
               </grid>
               <vitrification>
                  <cryogen_name>NONE</cryogen_name>
                  <instrument>OTHER</instrument>
               </vitrification>
            </single_particle_preparation>
         </specimen_preparation_list>
         <microscopy_list>
            <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">120</acceleration_voltage>
               <nominal_cs units="mm">2.0</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.6</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">0.92</nominal_defocus_max>
               <nominal_magnification>100000.0</nominal_magnification>
               <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
               <alignment_procedure>
                  <legacy>
                     <astigmatism>objective astigmatism corrected at 100,000 mag</astigmatism>
                     <electron_beam_tilt_params>-2</electron_beam_tilt_params>
                  </legacy>
               </alignment_procedure>
               <details>Images collected in 5 degree increments from 0 to -55</details>
               <date>2012-06-12</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GENERIC GATAN (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">0.109</sampling_interval>
                     </digitization_details>
                     <number_real_images>1095</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                     <details>Data collected on CCD</details>
                     <bits_per_pixel>16.</bits_per_pixel>
                  </image_recording>
               </image_recording_list>
               <tilt_angle_min>-50</tilt_angle_min>
               <tilt_angle_max>0</tilt_angle_max>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <ctf_correction>
               <details>Not corrected</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C3</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">20.0</resolution>
               <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN</name>
                  </software>
               </software_list>
               <details>Particles picked automatically using DoG-picker and cleaned up with reference free 2D class averaging</details>
               <number_images_used>8831</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="16001">
      <file>emd_2331.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>160</col>
         <row>160</row>
         <sec>160</sec>
      </dimensions>
      <origin>
         <col>-37</col>
         <row>-37</row>
         <sec>-37</sec>
      </origin>
      <spacing>
         <x>160</x>
         <y>160</y>
         <z>160</z>
      </spacing>
      <cell>
         <a units="&#8491;">348.80002</a>
         <b units="&#8491;">348.80002</b>
         <c units="&#8491;">348.80002</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>-4.59452868</minimum>
         <maximum>8.87144661</maximum>
         <average>0.0</average>
         <std>0.64018303</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.18</x>
         <y units="&#8491;">2.18</y>
         <z units="&#8491;">2.18</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>1.96</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Reconstruction of PGT135-BG505 SOSIP complex</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2331::::</details>
   </map>
   <interpretation>
      <figure_list>
         <figure>
            <file>emd_2331.png</file>
         </figure>
      </figure_list>
   </interpretation>
</emd>