<emd emdb_id="EMD-5352" 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>2011-11-02</deposition>
            <header_release>2011-11-28</header_release>
            <map_release>2012-02-20</map_release>
            <update>2012-03-06</update>
        </key_dates>
        <title>Structure of a type III secretion needle</title>
        <authors_list>
            <author>Fujii T</author>
            <author>Cheung M</author>
            <author>Blanco A</author>
            <author>Kato T</author>
            <author>Blocker AJ</author>
            <author>Namba K</author>
        </authors_list>
        <keywords>type III secretion system, needle, helical filament</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Fujii T</author>
                    <author order="2">Cheung M</author>
                    <author order="3">Blanco A</author>
                    <author order="4">Kato T</author>
                    <author order="5">Blocker AJ</author>
                    <author order="6">Namba K</author>
                    <title>Structure of a type III secretion needle at 7-A resolution provides insights into its assembly and signaling mechanisms.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>109</volume>
                    <first_page>4461</first_page>
                    <last_page>4466</last_page>
                    <year>2012</year>
                    <external_references type="PUBMED">22388746</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1116126109</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3j0r</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Shigella needle</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Shigella needle</name>
                <oligomeric_state>helical assembly of MxiH</oligomeric_state>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="MxiH">MxiH</name>
                <natural_source database="NCBI">
                    <organism ncbi="623">Shigella flexneri</organism>
                </natural_source>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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">
                    <buffer>
                        <ph>7.4</ph>
                        <details>20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4</details>
                    </buffer>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <instrument>OTHER</instrument>
                        <details>Vitrification instrument: Vitrobot</details>
                        <method>Blot for 3.5 seconds before plunging</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>JEOL 3200FSC</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">1.6</nominal_cs>
                    <nominal_defocus_min units="&#181;m">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>89285.0</calibrated_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">50</temperature_min>
                        <temperature_max units="K">60</temperature_max>
                        <temperature_average units="K">50</temperature_average>
                    </temperature>
                    <specialist_optics>
                        <energy_filter>
                            <name>JEOL Omega filter</name>
                            <lower_energy_threshold units="eV">0.0</lower_energy_threshold>
                            <upper_energy_threshold units="eV">10.0</upper_energy_threshold>
                        </energy_filter>
                    </specialist_optics>
                    <date>2008-07-02</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">TVIPS TEMCAM-F415 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>330</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">20</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>top entry</specimen_holder>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">4.30</delta_z>
                            <delta_phi units="deg">64.06</delta_phi>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>OTHER</algorithm>
                    <resolution res_type="BY AUTHOR" units="&#8491;">7.7</resolution>
                    <resolution_method>FSC 0.5 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                </final_reconstruction>
                <ctf_correction>
                    <details>CTFFIND3 Each particle</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="3908">
        <file>emd_5352.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>100</col>
            <row>100</row>
            <sec>100</sec>
        </dimensions>
        <origin>
            <col>-50</col>
            <row>-50</row>
            <sec>-50</sec>
        </origin>
        <spacing>
            <x>100</x>
            <y>100</y>
            <z>100</z>
        </spacing>
        <cell>
            <a units="&#8491;">168.0</a>
            <b units="&#8491;">168.0</b>
            <c units="&#8491;">168.0</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>-11.36894798</minimum>
            <maximum>22.53497505</maximum>
            <average>0.10644222</average>
            <std>2.6820209</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.68</x>
            <y units="&#8491;">1.68</y>
            <z units="&#8491;">1.68</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>6.76</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is an reconstruction of the type III secretion needle</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5352::::</details>
    </map>
</emd>