<emd emdb_id="EMD-2480" 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>2013-09-27</deposition>
            <header_release>2013-11-13</header_release>
            <map_release>2013-12-11</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Tomogram of Injectisome (wild type) from Salmonella typhiumurium (substrate trapped) in situ</title>
        <authors_list>
            <author>Radics J</author>
            <author>Konigsmaier L</author>
            <author>Marlovits TC</author>
        </authors_list>
        <keywords>Injectisome, Pathogenic Type-3 Secretion System, Protein delivery machine, Salmonella typhimurium, cryo electron tomography</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Radics J</author>
                    <author order="2">Koenigsmaier L</author>
                    <author order="3">Marlovits TC</author>
                    <title>Structure of a pathogenic type 3 secretion system in action.</title>
                    <journal>NAT.STRUCT.MOL.BIOL.</journal>
                    <volume>21</volume>
                    <first_page>82</first_page>
                    <last_page>87</last_page>
                    <year>2014</year>
                    <external_references type="PUBMED">24317488</external_references>
                    <external_references type="DOI">doi:10.1038/nsmb.2722</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Type-3 secretion system from Salmonella typhimurium in situ (substrate trapped): Visualization of unfolded protein transport across membranes</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Type-3 secretion system from Salmonella typhimurium in situ (substrate trapped): Visualization of unfolded protein transport across membranes</name>
                <oligomeric_state>1</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <theoretical units="MDa">3.5</theoretical>
                </molecular_weight>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name synonym="injectisome">type 3 secretion system</name>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="90371">Salmonella enterica subsp. enterica serovar Typhimurium</organism>
                    <strain>SB905</strain>
                    <cellular_location>Plasma membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">3.5</theoretical>
                </molecular_weight>
                <recombinant_expression database="NCBI" />
            </organelle_or_cellular_component_supramolecule>
        </supramolecule_list>
    </sample>
    <structure_determination_list>
        <structure_determination structure_determination_id="1">
            <method>tomography</method>
            <aggregation_state>cell</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <buffer>
                        <ph>8.0</ph>
                        <details>10 mM Tris, 5 mM EDTA</details>
                    </buffer>
                    <grid>
                        <details>400 mesh Mo-Grid Quantifoil R2/1</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">65</chamber_humidity>
                        <chamber_temperature units="K">91</chamber_temperature>
                        <instrument>LEICA EM GP</instrument>
                        <method>1. grids glowdischarged (300sec/20mAmp)
2. sample 5ul applied for 5sec (cell settling)
3. blotting for 2sec/distance 189</method>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI POLARA 300</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <nominal_cs units="mm">2</nominal_cs>
                    <nominal_defocus_max units="&#181;m">9.0</nominal_defocus_max>
                    <nominal_magnification>23000.0</nominal_magnification>
                    <calibrated_magnification>30120.0</calibrated_magnification>
                    <specimen_holder_model>GATAN HELIUM</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">83</temperature_min>
                        <temperature_max units="K">108</temperature_max>
                        <temperature_average units="K">93</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>objective lens astigmatism was corrected at appr 200.000 magnification</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2012-03-02</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN ULTRASCAN 4000 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>60</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">100</average_electron_dose_per_image>
                            <details>Image acquisition using SerialEM</details>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>liquid nitrogen cooled</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <max_angle units="deg">60</max_angle>
                            <angle_increment units="deg">2</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <details>IMOD (weighted back-projection)</details>
                <final_reconstruction>
                    <algorithm>OTHER</algorithm>
                    <software_list>
                        <software>
                            <name>IMOD</name>
                        </software>
                    </software_list>
                    <number_images_used>60</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="54693">
        <file>emd_2480.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED BYTE</data_type>
        <dimensions>
            <col>722</col>
            <row>768</row>
            <sec>101</sec>
        </dimensions>
        <origin>
            <col>-302</col>
            <row>-1</row>
            <sec>47</sec>
        </origin>
        <spacing>
            <x>768</x>
            <y>722</y>
            <z>101</z>
        </spacing>
        <cell>
            <a units="&#8491;">14353.359</a>
            <b units="&#8491;">15267.84</b>
            <c units="&#8491;">2007.8799</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>-128.0</minimum>
            <maximum>127.0</maximum>
            <average>-64.995986939999995</average>
            <std>3.70534849</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">19.88</x>
            <y units="&#8491;">19.88</y>
            <z units="&#8491;">19.88</z>
        </pixel_spacing>
        <annotation_details>Tomogram of substrate trapped type-3 secretion systems from Salmonella typhimurium</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2480::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2480.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>