<emd emdb_id="EMD-2700" 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>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2014-07-07</deposition>
            <header_release>2014-07-23</header_release>
            <map_release>2014-07-23</map_release>
            <update>2014-08-27</update>
        </key_dates>
        <title>Cryo-EM structure of the CTP synthetase filament</title>
        <authors_list>
            <author>Kollman JM</author>
            <author>Charles EJ</author>
            <author>Hansen JM</author>
        </authors_list>
        <keywords>nucleotide biosynthesis, enzyme polymerization, enzyme regulation, CTP, UTP, ATP</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Barry RM</author>
                    <author order="2">Bitbol A-F</author>
                    <author order="3">Lorestani A</author>
                    <author order="4">Charles EJ</author>
                    <author order="5">Habrian CH</author>
                    <author order="6">Hansen JM</author>
                    <author order="7">Li H-J</author>
                    <author order="8">Baldwin EP</author>
                    <author order="9">Wingreen NS</author>
                    <author order="10">Kollman JM</author>
                    <author order="11">Gitai Z</author>
                    <title>Large-scale filament formation inhibits the activity of CTP synthetase</title>
                    <journal>elife</journal>
                    <volume>3</volume>
                    <first_page>e03638</first_page>
                    <last_page>e03638</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">25030911</external_references>
                    <external_references type="DOI">doi:10.7554/eLife.03638</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>CTP synthetase filament</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>CTP synthetase filament</name>
                <details>Filament assembled from CTP synthetase incubated with substrates.</details>
                <oligomeric_state>helical polymer of CTP synthetase homotetramers</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="CTP synthase, CtpS">CTP synthetase</name>
                <natural_source database="NCBI">
                    <organism ncbi="562">Escherichia coli</organism>
                    <cellular_location>cytoplasm</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.056</experimental>
                </molecular_weight>
                <details>CtpS was incubated in the presence of substrates, and filament form as the product CTP builds up in the reaction</details>
                <number_of_copies>4</number_of_copies>
                <oligomeric_state>2-2-2 tetramer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                </recombinant_expression>
                <sequence />
            </protein_or_peptide>
        </macromolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>helical</method>
            <aggregation_state>filament</aggregation_state>
            <specimen_preparation_list>
                <helical_preparation preparation_id="1">
                    <concentration units="mg/mL">0.85</concentration>
                    <buffer>
                        <ph>7.8</ph>
                        <details>50mM Tris pH 7.8, 10 mM MgCl2, 1mM UTP, 1mM ATP, 0.2 mM GTP, 5 mM glutamine</details>
                    </buffer>
                    <grid>
                        <details>200 mesh carbon grid with Quantifoil 2/2 support</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <method>3-6s blot time before plubging</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>94000.0</nominal_magnification>
                    <calibrated_magnification>94000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective astigmatism corrected at 150,000x mag</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2012-11-01</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <number_real_images>3000</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">25</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>Particle alignment, 3-D reconstruction, and helical and local point group symmetrization were carried out in SPIDER, and hsearch_lorentz was used for helical symmetry parameter searches.</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">79.4</delta_z>
                            <delta_phi units="deg">48.3</delta_phi>
                            <axial_symmetry>C2</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">8.4</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER, hsearch_lorentz, EMAN1, ctffind</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>per micrograph</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="54001">
        <file>emd_2700.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>240</col>
            <row>240</row>
            <sec>240</sec>
        </dimensions>
        <origin>
            <col>-120</col>
            <row>-120</row>
            <sec>-120</sec>
        </origin>
        <spacing>
            <x>240</x>
            <y>240</y>
            <z>240</z>
        </spacing>
        <cell>
            <a units="&#8491;">393.6</a>
            <b units="&#8491;">393.6</b>
            <c units="&#8491;">393.6</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>-2.38333011</minimum>
            <maximum>3.16936803</maximum>
            <average>-0.0128391</average>
            <std>0.25320092</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.64</x>
            <y units="&#8491;">1.64</y>
            <z units="&#8491;">1.64</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.53</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>reconstruction of CTP synthetase filament</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2700::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2AD5</access_code>
                    <chain>
                        <chain_id>A</chain_id>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Domains were fit independently using Chimera</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>