<emd emdb_id="EMD-1674" 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>2010-01-06</deposition>
            <header_release>2010-06-16</header_release>
            <map_release>2010-10-19</map_release>
            <update>2011-12-23</update>
        </key_dates>
        <title>The cryo-EM structure of actin filament in the presence of phosphate</title>
        <authors_list>
            <author>Murakami K</author>
            <author>Yasunaga T</author>
            <author>Noguchi TQ</author>
            <author>Uyeda TQ</author>
            <author>Wakabayashi T</author>
        </authors_list>
        <keywords>actin, cytoskeleton, cell adhesion, cellular signaling, cytokinesis, muscle</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Murakami K</author>
                    <author order="2">Yasunaga T</author>
                    <author order="3">Noguchi TQ</author>
                    <author order="4">Gomibuchi Y</author>
                    <author order="5">Ngo KX</author>
                    <author order="6">Uyeda TQ</author>
                    <author order="7">Wakabayashi T</author>
                    <title>Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.</title>
                    <journal>CELL(CAMBRIDGE,MASS.)</journal>
                    <volume>143</volume>
                    <first_page>275</first_page>
                    <last_page>287</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20946985</external_references>
                    <external_references type="DOI">doi:10.1016/j.cell.2010.09.034</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3g37</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Actin filament in the presence of phosphate</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Actin filament in the presence of phosphate</name>
                <oligomeric_state>Filament</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">1.17</theoretical>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Actin">Actin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9986">Oryctolagus cuniculus</organism>
                    <synonym_organism>Rabbit</synonym_organism>
                    <tissue>Muscle</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.045</theoretical>
                </molecular_weight>
                <number_of_copies>26</number_of_copies>
                <oligomeric_state>Filament</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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">
                    <buffer>
                        <ph>7.4</ph>
                        <details>50 mM NaCl, 5 mM MgCl2, 0.025 mM ATP, 10 mM sodium phosphate (pH 7.4), 0.05 %NaN3, and 0.7 mM DTT</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">77</chamber_temperature>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>HITACHI EF2000</microscope>
                    <illumination_mode>SPOT SCAN</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">1.5</nominal_defocus_max>
                    <nominal_magnification>100000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">77</temperature_min>
                        <temperature_max units="K">77</temperature_max>
                        <temperature_average units="K">77</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>HITACH</name>
                        </energy_filter>
                    </specialist_optics>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GENERIC CCD</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">2.275</sampling_interval>
                            </digitization_details>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry liquid nitrogen-cooled cryo specimen holder</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">6.0</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>EOS</name>
                        </software>
                    </software_list>
                    <number_images_used>8000</number_images_used>
                </final_reconstruction>
                <final_two_d_classification>
                    <number_classes>72</number_classes>
                </final_two_d_classification>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="6922">
        <file>emd_1674.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>121</col>
            <row>121</row>
            <sec>121</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>121</x>
            <y>121</y>
            <z>121</z>
        </spacing>
        <cell>
            <a units="&#8491;">275.275</a>
            <b units="&#8491;">275.275</b>
            <c units="&#8491;">275.275</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>Y</fast>
            <medium>X</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-66.216200000000001</minimum>
            <maximum>105.405000000000001</maximum>
            <average>0.454097</average>
            <std>12.051</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.275</x>
            <y units="&#8491;">2.275</y>
            <z units="&#8491;">2.275</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>33.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is an image of a surface with B-factor correction.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-1674::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>O, NAMD, EOS</name>
                    </software>
                </software_list>
                <details>Protocol: Real-space refinement. The initial model was docked manually and refined using O, NAMD, and EOS.</details>
                <target_criteria>R-factor</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>