<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-5634" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>HPUB</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>PDBj</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>PDBj</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-04-06</deposition>
            <header_release>2013-10-16</header_release>
            <obsolete>2014-06-25</obsolete>
            <update>2014-06-25</update>
        </key_dates>
        <title>Cryo-EM structure of full-length dodecameric human Tip49a-Trx/Tip49b complex</title>
        <authors_list>
            <author>Song F</author>
            <author>Zhu P</author>
        </authors_list>
        <keywords>Tip49a, Tip49b, Ruvbl1, Ruvbl2, Pontin, Reptin, AMP-PNP, AAA+, Domain II, ATPase, Chromatin remodelling, Thioredoxin</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="false">
                    <author order="1">Song F</author>
                    <author order="2">Zhu P</author>
                    <title>Cryo-EM structure of full-length dodecameric human Tip49a/Tip49b complex</title>
                    <journal>To Be Published</journal>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Chimeric human chromatin remodelling Tip49a-Trx/Tip49b complex</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Chimeric human chromatin remodelling Tip49a-Trx/Tip49b complex</name>
                <oligomeric_state>One homohexamer of Tip49a-Trx binds to one homohexamer of Tip49b</oligomeric_state>
                <number_unique_components>3</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">0.74</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Ruvbl1, Pontin, TIP49, ECP54, INO80H">Tip49a</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <cellular_location>Nucleus</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.05</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Rosetta (DE3) pLysS</recombinant_strain>
                    <recombinant_plasmid>pRSF Duet-1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q9Y265</external_references>
                    <external_references type="GO">GO:0035267</external_references>
                    <external_references type="INTERPRO">IPR003593</external_references>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name synonym="Trx">Thioredoxin</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <synonym_organism>E.coli</synonym_organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.012</theoretical>
                </molecular_weight>
                <details>Fused to the C-terminal of Tip49a</details>
                <number_of_copies>6</number_of_copies>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Rosetta (DE3) pLysS</recombinant_strain>
                    <recombinant_plasmid>pRSF Duet-1</recombinant_plasmid>
                </recombinant_expression>
                <sequence/>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name synonym="Ruvbl2, Reptin, TIP48, ECP51, INO80J">Tip49b</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <cellular_location>Nucleus</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.05</theoretical>
                </molecular_weight>
                <number_of_copies>6</number_of_copies>
                <oligomeric_state>Hexamer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                    <recombinant_strain>Rosetta (DE3) pLysS</recombinant_strain>
                    <recombinant_plasmid>pRSF Duet-1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">Q9Y230</external_references>
                    <external_references type="GO">GO:0032508</external_references>
                    <external_references type="INTERPRO">IPR010339</external_references>
                </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">1</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <details>200mM NaCl, 25mM Tris-HCl, 1mM PMSF, 1mM DTT, 4mM MgCl2, 3mM AMP-PNP</details>
                    </buffer>
                    <grid>
                        <details>Quantifoil R2/1 300 mesh grid</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">100</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>Blot for 4.5 seconds before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI 20</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_cs units="mm">2.5</nominal_cs>
                    <nominal_defocus_min units="µm">1.5</nominal_defocus_min>
                    <nominal_defocus_max units="µm">3.9</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">85</temperature_min>
                    </temperature>
                    <date>2011-11-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 1000 (2k x 2k)</film_or_detector_model>
                            <number_real_images>230</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">20</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Gatan CT3500</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>CTF correction of each whole micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">19.0</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EMAN1, EMAN2</name>
                        </software>
                    </software_list>
                    <number_images_used>8825</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>1643</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="68658">
        <file>emd_5634.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>260</col>
            <row>260</row>
            <sec>260</sec>
        </dimensions>
        <origin>
            <col>-32</col>
            <row>-32</row>
            <sec>-32</sec>
        </origin>
        <spacing>
            <x>260</x>
            <y>260</y>
            <z>260</z>
        </spacing>
        <cell>
            <a units="Å">520.0</a>
            <b units="Å">520.0</b>
            <c units="Å">520.0</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>-23.59035873</minimum>
            <maximum>32.87937927</maximum>
            <average>0.0</average>
            <std>0.99999994</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">2.0</x>
            <y units="Å">2.0</y>
            <z units="Å">2.0</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>9.15</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Reconstruction of Chimeric Tip49a-Trx/Tip49b dodecameric complex</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5634::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3J3J</access_code>
                    <chain>
                        <chain_id>B</chain_id>
                    </chain>
                </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>
        <figure_list>
            <figure>
                <file>emd_5634.png</file>
            </figure>
            <figure>
                <file>emd_5634_1.png</file>
            </figure>
            <figure>
                <file>emd_5634_2.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>
