<emd emdb_id="EMD-6291" 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>2015-02-28</deposition>
            <header_release>2015-05-27</header_release>
            <map_release>2016-02-17</map_release>
            <update>2016-04-13</update>
        </key_dates>
        <title>16 Angstrom cryo-EM reconstruction of the alpha, beta, gamma TF55 chaperonin</title>
        <authors_list>
            <author>Chaston JJ</author>
            <author>Stewart AG</author>
            <author>Smits C</author>
            <author>Aragao D</author>
            <author>Struwe W</author>
            <author>Benesch J</author>
            <author>Xwong A</author>
            <author>Ling M</author>
            <author>Ashsan B</author>
            <author>Sandin S</author>
            <author>Rhodes D</author>
            <author>Molugu SK</author>
            <author>Molugu SK</author>
            <author>Bernal RA</author>
            <author>Stock D</author>
        </authors_list>
        <keywords>TF55 chaperonin, protein folding, Sulfolobus solfataricus, cryo-EM</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Chaston JJ</author>
                    <author order="2">Smits C</author>
                    <author order="3">Aragao D</author>
                    <author order="4">Wong ASW</author>
                    <author order="5">Ashsan B</author>
                    <author order="6">Sandin S</author>
                    <author order="7">Molugu SK</author>
                    <author order="8">Molugu SK</author>
                    <author order="9">Bernal RA</author>
                    <author order="10">Stock D</author>
                    <author order="11">Stewart AG</author>
                    <title>Structural and Functional Insights into the Evolution and Stress Adaptation of Type II Chaperonins</title>
                    <journal>STRUCTURE</journal>
                    <volume>24</volume>
                    <first_page>364</first_page>
                    <last_page>374</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26853941</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2015.12.016</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Cryo-EM reconstruction of the TF55 chaperonin containing the alpha, beta and gamma subunits</name>
                <oligomeric_state>Octadecamer composed of 6 alpha, 6 beta, and 6 gamma subunits per complex</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">1.08</theoretical>
                    <method>sequence</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>TF55 chaperonin</name>
                <natural_source database="NCBI">
                    <organism ncbi="2287">Sulfolobus solfataricus</organism>
                    <strain>DSM1617</strain>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">1</theoretical>
                </molecular_weight>
                <details>The TF55 chaperonin is composed of three proteins (alpha, beta, and gamma) arranged in an alternating fashion to form a 9-subunit ring (3 of each protein) which then stacks back-to-back with a second ring, forming an 18-subunit complex.</details>
                <number_of_copies>18</number_of_copies>
                <oligomeric_state>octadecamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                    <recombinant_plasmid>pETDUET (Novagen)</recombinant_plasmid>
                </recombinant_expression>
                <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">
                    <concentration units="mg/mL">0.5</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>20 mM Tris-Cl, pH 8.0, 2 mM MgCl2, 1 mM EDTA, 50 mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>400-mesh copper grid with holey carbon film support (Quantifoil R2/2)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">80</chamber_humidity>
                        <chamber_temperature units="K">108</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <method>3 microliters of sample were blotted off the Quantifoil R2/2 grid for 3 seconds before plunging.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FS</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">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.8</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">4.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <calibrated_magnification>69000.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">83</temperature_min>
                        <temperature_max units="K">103</temperature_max>
                        <temperature_average units="K">93</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 250,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <specialist_optics>
                        <energy_filter>
                            <name>JEOL in-column</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>2014-06-20</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>16534</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                            <bits_per_pixel>8.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>626 Gatan holder</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particle selection was performed using the e2boxer.py component of the EMAN2. Data was ctf-corrected using the ctfit algorithm and refined using EMAN.</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">16.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN, EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>16534</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>100</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_6291.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>-59</col>
            <row>-59</row>
            <sec>-59</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">347.84</a>
            <b units="&#8491;">347.84</b>
            <c units="&#8491;">347.84</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>-4.29047346</minimum>
            <maximum>8.94482517</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.174</x>
            <y units="&#8491;">2.174</y>
            <z units="&#8491;">2.174</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.2</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Cryo-EM reconstruction of the Sulfolobus solfataricus TF55 alpha/beta/gamma chaperonin</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6291::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6291.jpg</file>
            </figure>
        </figure_list>
    </interpretation>
    <validation>
        <fsc_curve>
            <file>emd_6291_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>