<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-3061" 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>2015-06-23</deposition>
         <header_release>2015-07-01</header_release>
         <map_release>2015-08-12</map_release>
         <update>2015-09-09</update>
      </key_dates>
      <title>Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution.</title>
      <authors_list>
         <author>Bai XC</author>
         <author>Yan CY</author>
         <author>Yang GH</author>
         <author>Lu PL</author>
         <author>Ma D</author>
         <author>Sun LF</author>
         <author>Zhou R</author>
         <author>Scheres SHW</author>
         <author>Shi YG</author>
      </authors_list>
      <keywords>cryo-EM, human gamma-secretase, membrane protein, single particle</keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Bai XC</author>
               <author order="2">Yan CY</author>
               <author order="3">Yang GH</author>
               <author order="4">Lu PL</author>
               <author order="5">Ma D</author>
               <author order="6">Sun LF</author>
               <author order="7">Zhou R</author>
               <author order="8">Scheres SHW</author>
               <author order="9">Shi YG</author>
               <title>An atomic structure of human gamma-secretase</title>
               <journal>NATURE</journal>
               <volume>525</volume>
               <first_page>212</first_page>
               <last_page>217</last_page>
               <year>2015</year>
               <external_references type="PUBMED">26280335</external_references>
               <external_references type="DOI">doi:10.1038/NATURE14892</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
      <pdb_list>
         <pdb_reference>
            <pdb_id>5a63</pdb_id>
            <relationship>
               <in_frame>FULLOVERLAP</in_frame>
            </relationship>
         </pdb_reference>
      </pdb_list>
   </crossreferences>
   <sample>
      <name>human gamma-secretase</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>human gamma-secretase</name>
            <oligomeric_state>heterotetramer</oligomeric_state>
            <number_unique_components>4</number_unique_components>
            <molecular_weight>
               <experimental units="MDa">0.17</experimental>
               <theoretical units="MDa">0.17</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name>gamma-secretase</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
               <cell>HEK 293F cells</cell>
               <cellular_location>membrane</cellular_location>
            </natural_source>
            <molecular_weight>
               <experimental units="MDa">0.17</experimental>
               <theoretical units="MDa">0.17</theoretical>
            </molecular_weight>
            <number_of_copies>1</number_of_copies>
            <oligomeric_state>Heterotetramer</oligomeric_state>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
               <recombinant_cell>HEK 293F cells</recombinant_cell>
               <recombinant_plasmid>pMLink</recombinant_plasmid>
            </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">6</concentration>
               <buffer>
                  <ph>7.4</ph>
                  <details>25 mM HEPES, pH 7.4, 150 mM NaCl and amphipol A8-35</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>cryo-EM</details>
               </staining>
               <grid>
                  <details>300 mesh Au 1.2/1.3 Quantifoil grid, glow discharged for 1 minute</details>
               </grid>
               <vitrification>
                  <cryogen_name>ETHANE</cryogen_name>
                  <chamber_humidity units="percentage">100</chamber_humidity>
                  <chamber_temperature units="K">85</chamber_temperature>
                  <instrument>FEI VITROBOT MARK IV</instrument>
                  <method>Blot for 4 seconds before plunging</method>
               </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">2.7</nominal_cs>
               <nominal_defocus_min units="&#181;m">0.7</nominal_defocus_min>
               <nominal_defocus_max units="&#181;m">3.2</nominal_defocus_max>
               <nominal_magnification>81000.0</nominal_magnification>
               <calibrated_magnification>35714.0</calibrated_magnification>
               <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
               <temperature>
                  <temperature_min units="K">80</temperature_min>
                  <temperature_max units="K">90</temperature_max>
                  <temperature_average units="K">85</temperature_average>
               </temperature>
               <specialist_optics>
                  <energy_filter>
                     <name>Gatan Quantum</name>
                     <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                     <upper_energy_threshold units="eV">20.0</upper_energy_threshold>
                  </energy_filter>
               </specialist_optics>
               <date>2014-10-02</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                     <digitization_details>
                        <sampling_interval units="&#181;m">5</sampling_interval>
                     </digitization_details>
                     <number_real_images>2925</number_real_images>
                     <average_electron_dose_per_image units="e/&#8491;^2">38</average_electron_dose_per_image>
                     <details>20 frames were recorded by the direct electron detector</details>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>Use a newly developed statistical movie processing and particle polishing approach to compensate for beam-induced movement and reduce the effect of radiation-damage.</details>
            <ctf_correction>
               <details>Each particle</details>
            </ctf_correction>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <resolution res_type="BY AUTHOR" units="&#8491;">3.4</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>CTFFIND3, RELION</name>
                  </software>
               </software_list>
               <number_images_used>159549</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="22783">
      <file>emd_3061.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="&#8491;">252.0</a>
         <b units="&#8491;">252.0</b>
         <c units="&#8491;">252.0</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>-0.2716414</minimum>
         <maximum>0.44705674</maximum>
         <average>0.0000526</average>
         <std>0.01502737</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">1.4</x>
         <y units="&#8491;">1.4</y>
         <z units="&#8491;">1.4</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.08</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>3D cryo-EM reconstruction of the human gamma-secretase complex at 3.4 angstrom resolution.</annotation_details>
      <details>::::EMDATABANK.org::::EMD-3061::::</details>
   </map>
</emd>