<emd emdb_id="EMD-3072" version="3.0.1.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 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>2015-07-01</deposition>
            <header_release>2015-07-15</header_release>
            <map_release>2015-09-30</map_release>
            <update>2016-03-02</update>
        </key_dates>
        <title>Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles</title>
        <authors_list>
            <author>Pfeffer S</author>
            <author>Burbaum L</author>
            <author>Unverdorben P</author>
            <author>Pech M</author>
            <author>Chen Y</author>
            <author>Zimmermann R</author>
            <author>Beckmann R</author>
            <author>Foerster F</author>
        </authors_list>
        <keywords>Ribosome, Sec61, Translocon, Endoplasmic Reticulum, Cryoelectron Tomography, Subtomogram Analysis</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Pfeffer S</author>
                    <author order="2">Burbaum L</author>
                    <author order="3">Unverdorben P</author>
                    <author order="4">Pech M</author>
                    <author order="5">Chen Y</author>
                    <author order="6">Zimmermann R</author>
                    <author order="7">Beckmann R</author>
                    <author order="8">Foerster F</author>
                    <title>Structure of the native Sec61 protein-conducting channel.</title>
                    <journal>NAT.COMMUN.</journal>
                    <volume>6</volume>
                    <first_page>8403</first_page>
                    <last_page>8403</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26411746</external_references>
                    <external_references type="DOI">doi:10.1038/ncomms9403</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles.</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles.</name>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
            <complex_supramolecule supramolecule_id="1">
                <name>Membrane-bound 80S ribosome</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="9615">Canis lupus familiaris</organism>
                    <synonym_organism>Dog</synonym_organism>
                    <tissue>Pancreas</tissue>
                </natural_source>
                <recombinant_expression database="NCBI" />
                <ribosome-details>ribosome-eukaryote: ALL</ribosome-details>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>ER protein translocon</name>
                <natural_source database="NCBI">
                    <organism ncbi="9615">Canis lupus familiaris</organism>
                    <synonym_organism>Dog</synonym_organism>
                    <tissue>Pancreas</tissue>
                    <organelle>Endoplasmic Reticulum</organelle>
                </natural_source>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <concentration units="mg/mL">2</concentration>
                    <buffer>
                        <ph>7.6</ph>
                        <details>20mM Hepes, 50mM KCl; 2mM MgCl2</details>
                    </buffer>
                    <grid>
                        <details>Lacey carbon molybdenum grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE-PROPANE MIXTURE</cryogen_name>
                        <chamber_humidity units="percentage">70</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot 3 seconds before plunging.</method>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_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_defocus_min units="&#181;m">3.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>Gatan</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2014-06-18</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-60</min_angle>
                            <max_angle units="deg">60</max_angle>
                            <angle_increment units="deg">2</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <details>Tomogram reconstruction was accomplished using PyTom.</details>
                <final_reconstruction>
                    <software_list>
                        <software>
                            <name>PyTom, tom_toolbox, av3_toolbox</name>
                        </software>
                    </software_list>
                    <number_images_used>61</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <details>Each tilt image</details>
                </ctf_correction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="106723">
        <file>emd_3072.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>462</col>
            <row>462</row>
            <sec>128</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>462</x>
            <y>462</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="&#8491;">9683.52</a>
            <b units="&#8491;">9683.52</b>
            <c units="&#8491;">2682.88</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>-25.035238270000001</minimum>
            <maximum>32.838691709999999</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">20.96</x>
            <y units="&#8491;">20.96</y>
            <z units="&#8491;">20.96</z>
        </pixel_spacing>
        <annotation_details>Representative tomogram of canine pancreatic rough Endoplasmic Reticulum vesicles.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-3072::::</details>
    </map>
</emd>