<emd emdb_id="EMD-6057" 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>2014-08-27</deposition>
            <header_release>2014-10-01</header_release>
            <map_release>2014-10-22</map_release>
            <update>2014-12-10</update>
        </key_dates>
        <title>Structure of the E. coli 50S subunit with ErmCL nascent chain</title>
        <authors_list>
            <author>Arenz S</author>
            <author>Meydan S</author>
            <author>Starosta AL</author>
            <author>Berninghausen O</author>
            <author>Beckmann R</author>
            <author>Vazquez-Laslop N</author>
            <author>Wilson DN</author>
        </authors_list>
        <keywords>erythromycin, stalling, RIBOSOME-ANTIBIOTIC complex, ErmCL</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Arenz S</author>
                    <author order="2">Meydan S</author>
                    <author order="3">Starosta AL</author>
                    <author order="4">Berninghausen O</author>
                    <author order="5">Beckmann R</author>
                    <author order="6">Vazquez-Laslop N</author>
                    <author order="7">Wilson DN</author>
                    <title>Drug-Sensing by the Ribosome Induces Translational Arrest via Active Site Perturbation.</title>
                    <journal>MOLECULAR CELL</journal>
                    <volume>56</volume>
                    <first_page>446</first_page>
                    <last_page>452</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25306253</external_references>
                    <external_references type="DOI">doi:10.1016/j.molcel.2014.09.014</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j7z</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>ErmCL-stalled E. coli ribosome</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>ErmCL-stalled E. coli ribosome</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <complex_supramolecule supramolecule_id="1">
                <name>50S ribosomal subunit</name>
                <details>ErmCL-stalled</details>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="83333">Escherichia coli K-12</organism>
                </natural_source>
                <recombinant_expression database="NCBI" />
                <ribosome-details>ribosome-prokaryote: LSU 50S</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>7.4</ph>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <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>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">0</nominal_cs>
                    <nominal_magnification>125085.0</nominal_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <date>2014-03-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">FEI FALCON II (4k x 4k)</film_or_detector_model>
                            <number_real_images>6118</number_real_images>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>defocus groups</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">3.9</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                    <details>Since the microscopy images were processed in the absence of spatial frequencies higher than 8 A, an FSC cut-off value of 0.143 was used for average resolution determination of 3.9 A (Scheres and Chen, 2012).</details>
                    <number_images_used>269163</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="29229">
        <file>emd_6057.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>177</col>
            <row>183</row>
            <sec>231</sec>
        </dimensions>
        <origin>
            <col>70</col>
            <row>92</row>
            <sec>79</sec>
        </origin>
        <spacing>
            <x>183</x>
            <y>177</y>
            <z>231</z>
        </spacing>
        <cell>
            <a units="&#8491;">196.11601</a>
            <b units="&#8491;">202.764</b>
            <c units="&#8491;">255.94801</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>-0.01293502</minimum>
            <maximum>0.01906713</maximum>
            <average>0.00029695</average>
            <std>0.00148553</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.108</x>
            <y units="&#8491;">1.108</y>
            <z units="&#8491;">1.108</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.003</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of ErmCL-stalled ribosome complex (30S masked out)</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6057::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4KIX</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>The crystal structure of the E. coli 50S subunit was fitted as a rigid body.</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>