<emd emdb_id="EMD-6583" 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>2016-01-20</deposition>
            <header_release>2016-03-09</header_release>
            <map_release>2016-07-20</map_release>
            <update>2016-08-24</update>
        </key_dates>
        <title>Cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania</title>
        <authors_list>
            <author>Shalev-Benami M</author>
            <author>Zhang Y</author>
            <author>Matzov D</author>
            <author>Halfon Y</author>
            <author>Zackay A</author>
            <author>Rozenberg H</author>
            <author>Zimmerman E</author>
            <author>Bashan A</author>
            <author>Jaffe CL</author>
            <author>Yonath A</author>
            <author>Skiniotis G</author>
        </authors_list>
        <keywords>The large ribosomal subunit from Leishmania donovani</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Shalev-Benami M</author>
                    <author order="2">Zhang Y</author>
                    <author order="3">Matzov D</author>
                    <author order="4">Halfon Y</author>
                    <author order="5">Zackay A</author>
                    <author order="6">Rozenberg H</author>
                    <author order="7">Zimmerman E</author>
                    <author order="8">Bashan A</author>
                    <author order="9">Jaffe CL</author>
                    <author order="10">Yonath A</author>
                    <author order="11">Skiniotis G</author>
                    <title>2.8-A Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania.</title>
                    <journal>CELL REPORTS</journal>
                    <volume>16</volume>
                    <first_page>288</first_page>
                    <last_page>294</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27373148</external_references>
                    <external_references type="DOI">doi:10.1016/j.celrep.2016.06.014</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3jcs</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Leishimania donovani 91S ribosome</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Leishimania donovani 91S ribosome</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <complex_supramolecule supramolecule_id="1">
                <name>91S ribosome</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="5661">Leishmania donovani</organism>
                    <cellular_location>cytoplasm</cellular_location>
                </natural_source>
                <recombinant_expression database="NCBI" />
                <ribosome-details>ribosome-eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S</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">
                    <concentration units="mg/mL">0.3</concentration>
                    <buffer>
                        <ph>7.6</ph>
                        <details>20 mM HEPES-KOH, pH 7.6, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc, 1 mM DTT</details>
                    </buffer>
                    <grid>
                        <details>25 seconds on glow-discharged holey carbon grids (Quantifoil R2/2) coated with continuous thin carbon film</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                    </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_defocus_min units="&#181;m">0.6</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.5</nominal_defocus_max>
                    <nominal_magnification>29000.0</nominal_magnification>
                    <calibrated_magnification>25000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <specialist_optics>
                        <energy_filter>
                            <name>FEI</name>
                        </energy_filter>
                    </specialist_optics>
                    <date>2015-07-07</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">2.8</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>107134</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="221185">
        <file>emd_6583.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>384</col>
            <row>384</row>
            <sec>384</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>384</x>
            <y>384</y>
            <z>384</z>
        </spacing>
        <cell>
            <a units="&#8491;">384.0</a>
            <b units="&#8491;">384.0</b>
            <c units="&#8491;">384.0</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>-0.11835618</minimum>
            <maximum>0.2307336</maximum>
            <average>0.00044537</average>
            <std>0.00627039</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.0</x>
            <y units="&#8491;">1.0</y>
            <z units="&#8491;">1.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.02</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of the large ribosomal subunit from the eukaryotic parasite Leishmania donovani</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6583::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6583.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>