<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" emdb_id="EMD-2478" 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>2013-09-23</deposition>
         <header_release>2013-11-13</header_release>
         <map_release>2013-11-20</map_release>
         <update>2016-03-02</update>
      </key_dates>
      <title>Negative stain electron microscopy structure of compound E-bound human Presenilin 1 (PS1) complex</title>
      <authors_list>
         <author>Li Y</author>
         <author>Lu S</author>
         <author>Tsai CJ</author>
         <author>Bohm C</author>
         <author>Qamar S</author>
         <author>Dodd RB</author>
         <author>Meadows W</author>
         <author>Jeon A</author>
         <author>McLeod A</author>
         <author>Chen F</author>
         <author>Arimon M</author>
         <author>Berezovska O</author>
         <author>Hyman BT</author>
         <author>Tomita T</author>
         <author>Iwatsubod T</author>
         <author>Johnsof CM</author>
         <author>Farrer L</author>
         <author>Schmitt-Ulms G</author>
         <author>Fraser P</author>
         <author>St George-Hyslop P</author>
      </authors_list>
      <keywords>
         </keywords>
   </admin>
   <crossreferences>
      <citation_list>
         <primary_citation>
            <journal_citation published="true">
               <author order="1">Li Y</author>
               <author order="2">Lu SH</author>
               <author order="3">Tsai CJ</author>
               <author order="4">Bohm C</author>
               <author order="5">Qamar S</author>
               <author order="6">Dodd RB</author>
               <author order="7">Meadows W</author>
               <author order="8">Jeon A</author>
               <author order="9">McLeod A</author>
               <author order="10">Chen F</author>
               <author order="11">Arimon M</author>
               <author order="12">Berezovska O</author>
               <author order="13">Hyman BT</author>
               <author order="14">Tomita T</author>
               <author order="15">Iwatsubo T</author>
               <author order="16">Johnson CM</author>
               <author order="17">Farrer LA</author>
               <author order="18">Schmitt-Ulms G</author>
               <author order="19">Fraser PE</author>
               <author order="20">St George-Hyslop PH</author>
               <title>Structural interactions between inhibitor and substrate docking sites give insight into mechanisms of human PS1 complexes.</title>
               <journal>STRUCTURE</journal>
               <volume>22</volume>
               <first_page>125</first_page>
               <last_page>135</last_page>
               <year>2014</year>
               <external_references type="PUBMED">24210759</external_references>
               <external_references type="DOI">doi:10.1016/j.str.2013.09.018</external_references>
            </journal_citation>
         </primary_citation>
      </citation_list>
   </crossreferences>
   <sample>
      <name>Compound E-bound human Presenilin 1 (PS1) complex</name>
      <supramolecule_list>
         <sample_supramolecule supramolecule_id="1000">
            <name>Compound E-bound human Presenilin 1 (PS1) complex</name>
            <details>The sample was monodisperse</details>
            <oligomeric_state>1:1:1:1</oligomeric_state>
            <number_unique_components>5</number_unique_components>
            <molecular_weight>
               <theoretical units="MDa">0.2</theoretical>
            </molecular_weight>
         </sample_supramolecule>
      </supramolecule_list>
      <macromolecule_list>
         <protein_or_peptide macromolecule_id="1">
            <name synonym="Protein S182">Presenilin-1</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
            </natural_source>
            <details>N-terminus as tagged with TAP tag composed of Protein G and Streptavidin binding peptide tags separated by tobacco etch virus protease cleavage site</details>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>true</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               <recombinant_organism ncbi="9606">Homo sapiens</recombinant_organism>
               <recombinant_cell>HEK293</recombinant_cell>
            </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">P49768</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="2">
            <name synonym="KIAA0253">Nicastrin</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
               <cell>HEK293</cell>
            </natural_source>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q92542</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="3">
            <name synonym="Aph-1alpha">Gamma-secretase subunit APH-1A</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
               <cell>HEK293</cell>
            </natural_source>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q96BI3</external_references>
            </sequence>
         </protein_or_peptide>
         <protein_or_peptide macromolecule_id="4">
            <name synonym="Presenilin enhancer protein 2">Gamma-secretase subunit PEN-2</name>
            <natural_source database="NCBI">
               <organism ncbi="9606">Homo sapiens</organism>
               <synonym_organism>Human</synonym_organism>
               <cell>HEK293</cell>
            </natural_source>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
            <sequence>
               <external_references type="UNIPROTKB">Q9NZ42</external_references>
            </sequence>
         </protein_or_peptide>
         <ligand macromolecule_id="5">
            <name synonym="gamma-Secretase Inhibitor XXI">E ((S,S)- 2-[2-(3,5-Difluorophenyl)-acetylamino]-N-(1-methyl-2-oxo-5-phenyl-2,3-dihydro-1H-benzo[e][1,4]diazepin-3-yl)-propionamide)</name>
            <natural_source database="NCBI">
               <organism ncbi="32630">synthetic construct</organism>
            </natural_source>
            <number_of_copies>1</number_of_copies>
            <recombinant_exp_flag>false</recombinant_exp_flag>
            <recombinant_expression database="NCBI">
               </recombinant_expression>
         </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">
               <concentration units="mg/mL">0.02</concentration>
               <buffer>
                  <ph>7.4</ph>
                  <details>50 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 5 mM MgCl2, 5 mM CaCl2</details>
               </buffer>
               <staining>
                  <type>NEGATIVE</type>
                  <details>Grids with adsorbed protein floated on 1% w/v uranyl acetate for 2-10 seconds</details>
               </staining>
               <grid>
                  <details>Carbon-coated 400-mesh copper grids were glow discharged in air at 600-700 V for 30-60 seconds on an Edward S150B sputter coater.</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 12</microscope>
               <illumination_mode>FLOOD BEAM</illumination_mode>
               <imaging_mode>BRIGHT FIELD</imaging_mode>
               <electron_source>TUNGSTEN HAIRPIN</electron_source>
               <acceleration_voltage units="kV">120</acceleration_voltage>
               <nominal_cs units="mm">2</nominal_cs>
               <nominal_defocus_max units="&#181;m">1.0</nominal_defocus_max>
               <specimen_holder_model>OTHER</specimen_holder_model>
               <date>2009-09-19</date>
               <image_recording_list>
                  <image_recording>
                     <film_or_detector_model category="CCD">TVIPS TEMCAM-F224 (2k x 2k)</film_or_detector_model>
                     <number_real_images>300</number_real_images>
                  </image_recording>
               </image_recording_list>
            </single_particle_microscopy>
         </microscopy_list>
         <singleparticle_processing image_processing_id="1">
            <details>The particles were selected using EMAN2</details>
            <final_reconstruction>
               <applied_symmetry>
                  <point_group>C1</point_group>
               </applied_symmetry>
               <algorithm>OTHER</algorithm>
               <resolution res_type="BY AUTHOR" units="&#8491;">17.4</resolution>
               <resolution_method>OTHER</resolution_method>
               <software_list>
                  <software>
                     <name>EMAN2, RELION</name>
                  </software>
               </software_list>
               <number_images_used>10651</number_images_used>
            </final_reconstruction>
         </singleparticle_processing>
      </structure_determination>
   </structure_determination_list>
   <map format="CCP4" size_kbytes="8193">
      <file>emd_2478.map.gz</file>
      <symmetry>
         <space_group>1</space_group>
      </symmetry>
      <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
      <dimensions>
         <col>128</col>
         <row>128</row>
         <sec>128</sec>
      </dimensions>
      <origin>
         <col>0</col>
         <row>0</row>
         <sec>0</sec>
      </origin>
      <spacing>
         <x>128</x>
         <y>128</y>
         <z>128</z>
      </spacing>
      <cell>
         <a units="&#8491;">261.12</a>
         <b units="&#8491;">261.12</b>
         <c units="&#8491;">261.12</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>-0.0298597</minimum>
         <maximum>0.05378654</maximum>
         <average>-0.00013971</average>
         <std>0.00514203</std>
      </statistics>
      <pixel_spacing>
         <x units="&#8491;">2.04</x>
         <y units="&#8491;">2.04</y>
         <z units="&#8491;">2.04</z>
      </pixel_spacing>
      <contour_list>
         <contour primary="true">
            <level>0.0155</level>
            <source>AUTHOR</source>
         </contour>
      </contour_list>
      <annotation_details>Native human PS1 complex</annotation_details>
      <details>::::EMDATABANK.org::::EMD-2478::::</details>
   </map>
</emd>