<emd emdb_id="EMD-5220" 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>2010-07-23</deposition>
            <header_release>2010-12-08</header_release>
            <map_release>2012-08-22</map_release>
            <update>2012-08-22</update>
        </key_dates>
        <title>The architecture of the DNA polymerase-PCNA-DNA ternary complex</title>
        <authors_list>
            <author>Mayanagi K</author>
            <author>Nishida H</author>
            <author>Kiyonari S</author>
            <author>Saito M</author>
            <author>Kohda D</author>
            <author>Ishino Y</author>
            <author>Shirai T</author>
            <author>Morikawa K</author>
        </authors_list>
        <keywords>DNA replication,DNA clamp</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Mayanagi K</author>
                    <author order="2">Kiyonari S</author>
                    <author order="3">Nishida H</author>
                    <author order="4">Saito M</author>
                    <author order="5">Kohda D</author>
                    <author order="6">Ishino Y</author>
                    <author order="7">Shirai T</author>
                    <author order="8">Morikawa K</author>
                    <title>Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>108</volume>
                    <first_page>1845</first_page>
                    <last_page>1849</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">21245343</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1010933108</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Pyrococcus furiosus PolB-PCNA-DNA</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Pyrococcus furiosus PolB-PCNA-DNA</name>
                <details>The sample was monodisperse</details>
                <oligomeric_state>One PolB binds to one trimer of PCNA and primed DNA</oligomeric_state>
                <number_unique_components>3</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.21</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="PolB">DNA polymerase</name>
                <natural_source database="NCBI">
                    <organism ncbi="2261">Pyrococcus furiosus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.104</theoretical>
                </molecular_weight>
                <oligomeric_state>monomer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="PCNA">proliferating cell nuclear antigen</name>
                <natural_source database="NCBI">
                    <organism ncbi="2261">Pyrococcus furiosus</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.104</theoretical>
                </molecular_weight>
                <oligomeric_state>trimer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <sequence />
            </protein_or_peptide>
            <dna macromolecule_id="3">
                <name synonym="DNA">DNA</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.023</theoretical>
                </molecular_weight>
                <classification>DNA</classification>
                <structure>DOUBLE HELIX</structure>
                <synthetic_flag>true</synthetic_flag>
            </dna>
        </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">0.02</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>50 mM Tris-HCl,5 mM MgCl2</details>
                    </buffer>
                    <grid>
                        <details>200 mesh Cu grid with carbon support film</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 1010</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>TUNGSTEN HAIRPIN</electron_source>
                    <acceleration_voltage units="kV">100</acceleration_voltage>
                    <nominal_magnification>400000.0</nominal_magnification>
                    <specimen_holder_model>JEOL</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective astigmatism was corrected using a quadrupole stigmator at 400,000 times magnification.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <details>minimum dose</details>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC GATAN</film_or_detector_model>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry standard</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">19.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN, IMAGIC</name>
                        </software>
                    </software_list>
                    <number_images_used>18897</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="687">
        <file>emd_5220.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>56</col>
            <row>56</row>
            <sec>56</sec>
        </dimensions>
        <origin>
            <col>-9</col>
            <row>-9</row>
            <sec>-9</sec>
        </origin>
        <spacing>
            <x>56</x>
            <y>56</y>
            <z>56</z>
        </spacing>
        <cell>
            <a units="&#8491;">173.59999</a>
            <b units="&#8491;">173.59999</b>
            <c units="&#8491;">173.59999</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>-3.8578527</minimum>
            <maximum>8.5686512</maximum>
            <average>-0.00000002</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">3.1</x>
            <y units="&#8491;">3.1</y>
            <z units="&#8491;">3.1</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.25</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a map of PolB-PCNA-DNA complex</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5220::::</details>
    </map>
</emd>