<emd emdb_id="EMD-5148" 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>2009-12-10</deposition>
            <header_release>2010-03-08</header_release>
            <map_release>2010-03-08</map_release>
            <update>2015-07-15</update>
        </key_dates>
        <title>4.0 Angstrom two-fold imposed cryo-EM map of TRiC in the both-ring closed ATP-AlFx state</title>
        <authors_list>
            <author>Cong Y</author>
            <author>Baker ML</author>
            <author>Jakana J</author>
            <author>Woolford D</author>
            <author>Miller EJ</author>
            <author>Reissmann S</author>
            <author>Kumar RN</author>
            <author>Redding-Johanson AM</author>
            <author>Batth TS</author>
            <author>Mukhopadhyay A</author>
            <author>Ludtke SJ</author>
            <author>Frydman J</author>
            <author>Chiu W</author>
        </authors_list>
        <keywords>TRiC/CCT, Asymmetric, Cryo-EM, structure</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Cong Y</author>
                    <author order="2">Baker ML</author>
                    <author order="3">Jakana J</author>
                    <author order="4">Woolford D</author>
                    <author order="5">Miller EJ</author>
                    <author order="6">Reissmann S</author>
                    <author order="7">Kumar RN</author>
                    <author order="8">Redding-Johanson AM</author>
                    <author order="9">Batth TS</author>
                    <author order="10">Mukhopadhyay A</author>
                    <author order="11">Ludtke SJ</author>
                    <author order="12">Frydman J</author>
                    <author order="13">Chiu W</author>
                    <title>4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>107</volume>
                    <first_page>4967</first_page>
                    <last_page>4972</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20194787</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.0913774107</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3iyg</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
            <pdb_reference>
                <pdb_id>3ktt</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>bovine TRiC (also called CCT)</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>bovine TRiC (also called CCT)</name>
                <number_unique_components>8</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.5</experimental>
                    <theoretical units="MDa">0.45</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="TRiC or CCT">TRiC or CCT</name>
                <natural_source database="NCBI">
                    <organism ncbi="9913">Bos taurus</organism>
                    <synonym_organism>bovine</synonym_organism>
                </natural_source>
                <number_of_copies>8</number_of_copies>
                <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>singleParticle</method>
            <aggregation_state>particle</aggregation_state>
            <specimen_preparation_list>
                <single_particle_preparation preparation_id="1">
                    <grid>
                        <details>200-mesh Quantifoil holey grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">101</chamber_temperature>
                        <instrument>OTHER</instrument>
                        <method>two-side blotting for 1 second before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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_cs units="mm">4.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>JEOL 3200FSC CRYOHOLDER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">101</temperature_min>
                        <temperature_average units="K">101</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism correction</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>in-column omega energy filter</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">20.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2008-08-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>1500</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>side entry</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                    <details>A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps</details>
                    <number_images_used>101000</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="32769">
        <file>emd_5148.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>256</col>
            <row>256</row>
            <sec>128</sec>
        </dimensions>
        <origin>
            <col>-128</col>
            <row>-128</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>256</x>
            <y>256</y>
            <z>128</z>
        </spacing>
        <cell>
            <a units="&#8491;">307.2</a>
            <b units="&#8491;">307.2</b>
            <c units="&#8491;">153.6</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>-3.01933718</minimum>
            <maximum>7.45560551</maximum>
            <average>0.05451208</average>
            <std>0.37731904</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.2</x>
            <y units="&#8491;">1.2</y>
            <z units="&#8491;">1.2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.5</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>4.0 Angstrom two-fold imposed cryo-EM map of bovine TRiC in the closed conformation</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5148::::</details>
    </map>
</emd>