<emd emdb_id="EMD-5329" 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>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2011-07-12</deposition>
            <header_release>2011-07-28</header_release>
            <map_release>2011-11-09</map_release>
            <update>2013-03-06</update>
        </key_dates>
        <title>Cryo EM reconstruction of mammalian 80S ribosome in rotated PRE state 2</title>
        <authors_list>
            <author>Budkevich T</author>
            <author>Giesebrecht J</author>
            <author>Altman R</author>
            <author>Munro J</author>
            <author>Mielke T</author>
            <author>Nierhaus K</author>
            <author>Blanchard S</author>
            <author>Spahn C</author>
        </authors_list>
        <keywords>80S ribosome, mammalian, elongation cycle, tRNA</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Budkevich T</author>
                    <author order="2">Giesebrecht J</author>
                    <author order="3">Altman RB</author>
                    <author order="4">Munro JB</author>
                    <author order="5">Mielke T</author>
                    <author order="6">Nierhaus KH</author>
                    <author order="7">Blanchard SC</author>
                    <author order="8">Spahn CM</author>
                    <title>Structure and dynamics of the mammalian ribosomal pretranslocation complex.</title>
                    <journal>MOLECULAR CELL</journal>
                    <volume>44</volume>
                    <first_page>214</first_page>
                    <last_page>224</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">22017870</external_references>
                    <external_references type="DOI">doi:10.1016/j.molcel.2011.07.040</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j0q</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>80S-PRE-rotated-2 complex from rabbit (Oryctolagus cuniculus) liver</name>
                <details>Sample was re-associated from subunits</details>
                <oligomeric_state>monomer</oligomeric_state>
                <number_unique_components>5</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">4</experimental>
                    <method>Sedimentation</method>
                </molecular_weight>
            </sample_supramolecule>
            <complex_supramolecule supramolecule_id="1">
                <name>80S ribosome</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                    <synonym_organism>rabbit</synonym_organism>
                    <tissue>liver</tissue>
                </natural_source>
                <recombinant_expression database="NCBI" />
                <molecular_weight>
                    <theoretical units="MDa">4</theoretical>
                </molecular_weight>
                <ribosome-details>ribosome-eukaryote: LSU 60S, SSU 40S</ribosome-details>
            </complex_supramolecule>
        </supramolecule_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>
                    </buffer>
                    <grid>
                        <details>Quantifoil grids</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">77</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: VitroBot (FEI)</details>
                        <method>Flash-frozen in liquid ethane on carbon coated Quantifoil grids</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</microscope>
                    <illumination_mode>SPOT SCAN</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</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>39000.0</nominal_magnification>
                    <calibrated_magnification>65520.0</calibrated_magnification>
                    <specimen_holder_model>GATAN HELIUM</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">77</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 200,000 times magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2006-10-17</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">4.7</sampling_interval>
                            </digitization_details>
                            <number_real_images>87</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Cartridge</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>By defocus groups</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">10.6</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                    <details>Several rounds of multireference 3D projection refinement</details>
                    <number_images_used>23347</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="22783">
        <file>emd_5329.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>-90</col>
            <row>-90</row>
            <sec>-89</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="&#8491;">453.6</a>
            <b units="&#8491;">453.6</b>
            <c units="&#8491;">453.6</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>-2542.372802729999876</minimum>
            <maximum>17103.236328129998583</maximum>
            <average>275.671539310000014</average>
            <std>1215.576416019999897</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.52</x>
            <y units="&#8491;">2.52</y>
            <z units="&#8491;">2.52</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1000.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>80S mammalian ribosome</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5329::::</details>
    </map>
</emd>