<emd emdb_id="EMD-6339" 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>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2015-05-18</deposition>
            <header_release>2015-08-26</header_release>
            <map_release>2015-11-18</map_release>
            <update>2015-12-09</update>
        </key_dates>
        <title>Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA</title>
        <authors_list>
            <author>Lau WCY</author>
            <author>Li Y</author>
            <author>Zhang Q</author>
            <author>Huen MSY</author>
        </authors_list>
        <keywords>Translesion synthesis, DNA damage tolerance, Y-Family polymerase, PCNA monoubiquitination</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Lau WCY</author>
                    <author order="2">Li Y</author>
                    <author order="3">Zhang Q</author>
                    <author order="4">Huen MSY</author>
                    <title>Molecular architecture of the Ub-PCNA/Pol eta complex bound to DNA</title>
                    <journal>SCI REP</journal>
                    <volume>5</volume>
                    <first_page>15759</first_page>
                    <last_page>15759</last_page>
                    <year>2015</year>
                    <external_references type="PUBMED">26503230</external_references>
                    <external_references type="DOI">doi:10.1038/srep15759</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3ja9</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Ub-PCNA/Pol eta/DNA</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Ub-PCNA/Pol eta/DNA</name>
                <details>The sample was monodisperse</details>
                <oligomeric_state>Monomeric catalytic core of Pol eta binds to one homotrimeric Ub-PCNA</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.2</experimental>
                    <theoretical units="MDa">0.2</theoretical>
                    <method>Chemical crosslinking, SDS-PAGE</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Monoubiquitinated PCNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.12</experimental>
                    <theoretical units="MDa">0.12</theoretical>
                </molecular_weight>
                <oligomeric_state>trimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>BL21(DE3)</recombinant_strain>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>Pol eta</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                </natural_source>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>Monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>RW644</recombinant_strain>
                    <recombinant_plasmid>pJM879</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">0.1</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>50mM Tris-HCl, 5mM MgCl2</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>Grids with adsorbed protein floated on two 20ul drops of 2% w/v uranyl acetate solution for 30 seconds</details>
                    </staining>
                    <grid>
                        <details>Continuous carbon coated copper grids (Ted Pella), glow-discharged for 30 seconds</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 2010</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>SIDE ENTRY, EUCENTRIC</specimen_holder_model>
                    <date>2014-11-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <average_electron_dose_per_image units="e/&#8491;^2">18</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Particles</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">22.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>7330</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>227</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="4395">
        <file>emd_6339.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>104</col>
            <row>104</row>
            <sec>104</sec>
        </dimensions>
        <origin>
            <col>-52</col>
            <row>-52</row>
            <sec>-52</sec>
        </origin>
        <spacing>
            <x>104</x>
            <y>104</y>
            <z>104</z>
        </spacing>
        <cell>
            <a units="&#8491;">222.56001</a>
            <b units="&#8491;">222.56001</b>
            <c units="&#8491;">222.56001</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>-0.31146783</minimum>
            <maximum>2.77413011</maximum>
            <average>0.0</average>
            <std>0.31292593</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.14</x>
            <y units="&#8491;">2.14</y>
            <z units="&#8491;">2.14</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>1.27</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Ub-PCNA/Pol eta/DNA ternary complex</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6339::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1VYM</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
            <modelling>
                <initial_model>
                    <access_code>3MR2</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>