<?xml version="1.0" encoding="UTF-8"?>
<emd emdb_id="EMD-2384" version="3.0.1.9">
    <admin>
        <status_history_list>
            <status status_id="1">
                <code>REL</code>
            </status>
        </status_history_list>
        <current_status>
            <code>OBS</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2013-05-24</deposition>
            <header_release>2013-07-03</header_release>
            <map_release>2013-10-02</map_release>
            <obsolete>2013-10-02</obsolete>
            <update>2013-10-02</update>
        </key_dates>
        <title>Organization of protein complexes and a mechanism for grana formation in photosynthetic membranes as revealed by cryo-electron microscopy.</title>
        <authors_list>
            <author>Ford RC</author>
            <author>Holzenburg A</author>
        </authors_list>
        <keywords>Photosynthesis, thylakoid membrane, CF1-CF0 proton ATPase, photosystem, cytochrome b6f, ribosome, chloroplast.</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Ford RC</author>
                    <author order="2">Holzenburg A</author>
                    <title>Organization of protein complexes and a mechanism for grana formation in photosynthetic membranes as revealed by cryo-electron microscopy</title>
                    <journal>Crystal Research and Technology</journal>
                    <year>2013</year>
                    <external_references type="DOI">doi:10.1002/crat.201300116</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>Thylakoid membrane from spinach.</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Thylakoid membrane from spinach.</name>
                <number_unique_components>1</number_unique_components>
            </sample_supramolecule>
            <organelle_or_cellular_component_supramolecule supramolecule_id="1">
                <name synonym="Photosynthetic membrane">Thylakoid membrane</name>
                <details>Buffer - 20mM MES, 5mM MgCl2, 15mM NaCl, pH6.5, 150mM sorbitol. 3microlitres of membranes at 2mg per ml chlorophyll were directly applied to electron microscope grids (Quantifoil carbon grids with 1.2 micron holes). After blotting excess liquid, (2x 1s blots at 95 percent relative humidity in a Vitrobot device), the grids were rapidly frozen by plunging into liquid ethane and transferred at less than 110K to the Gatan cryo-stage of the electron microscope. 10nm fiducial gold particles were added.</details>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <natural_source database="NCBI">
                    <organism ncbi="3562">Spinacia oleracea</organism>
                    <synonym_organism>Spinach</synonym_organism>
                    <tissue>Leaf</tissue>
                    <organelle>Chloroplast</organelle>
                </natural_source>
                <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>tissue</aggregation_state>
            <specimen_preparation_list>
                <tomography_preparation preparation_id="1">
                    <concentration units="mg/mL">2</concentration>
                    <buffer>
                        <ph>6.5</ph>
                        <details>20mM MES, 5mM MgCl2, 15mM NaCl, pH6.5, 150mM sorbitol.</details>
                    </buffer>
                    <staining>
                        <type>NEGATIVE</type>
                        <details>No stain.</details>
                    </staining>
                    <grid>
                        <details>Quantifoil 400mesh carbon grids with 1.2 micron holes.</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>NITROGEN</cryogen_name>
                        <chamber_humidity units="percentage">95</chamber_humidity>
                        <chamber_temperature units="K">97</chamber_temperature>
                        <instrument>FEI VITROBOT MARK I</instrument>
                        <details>Vitrification instrument: Vitrobot FEI. Rapid plunging into liquid ethane.</details>
                        <method>2 x 1 sec blots before plunging.</method>
                    </vitrification>
                </tomography_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <tomography_microscopy microscopy_id="1">
                    <microscope>FEI TECNAI F20</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">2.0</nominal_cs>
                    <nominal_defocus_min units="µm">8.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">8.0</nominal_defocus_max>
                    <nominal_magnification>34000.0</nominal_magnification>
                    <calibrated_magnification>33998.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_min units="K">96</temperature_min>
                        <temperature_max units="K">98</temperature_max>
                        <temperature_average units="K">97</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Astigmatism corrected by live FFT.</astigmatism>
                        </legacy>
                    </alignment_procedure>
                    <date>2009-07-28</date>
                    <image_recording_list>
                        <image_recording>
                            <digitization_details>
                                <sampling_interval units="µm">15</sampling_interval>
                            </digitization_details>
                            <number_real_images>57</number_real_images>
                            <average_electron_dose_per_image units="e/Å^2">45</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Single tilt</specimen_holder>
                    <tilt_series>
                        <axis1>
                            <min_angle units="deg">-65</min_angle>
                            <max_angle units="deg">49</max_angle>
                            <angle_increment units="deg">1</angle_increment>
                        </axis1>
                    </tilt_series>
                </tomography_microscopy>
            </microscopy_list>
            <tomography_processing image_processing_id="1">
                <details>1 degree increments above 45 deg, 2.5 degree increments below this.</details>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">45.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>eTOMO</name>
                        </software>
                    </software_list>
                    <details>Standard eTOMO procedures for single axis tilt tomograms. Fiducials were selected from the tomogram and tracked in each image by hand initially.</details>
                    <number_images_used>57</number_images_used>
                </final_reconstruction>
            </tomography_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="97370">
        <file>emd_2384.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS SIGNED INTEGER (2 BYTES)</data_type>
        <dimensions>
            <col>690</col>
            <row>578</row>
            <sec>125</sec>
        </dimensions>
        <origin>
            <col>-57</col>
            <row>-87</row>
            <sec>6</sec>
        </origin>
        <spacing>
            <x>578</x>
            <y>690</y>
            <z>125</z>
        </spacing>
        <cell>
            <a units="Å">6072.0</a>
            <b units="Å">5086.4</b>
            <c units="Å">1100.0</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>23.0</minimum>
            <maximum>236.0</maximum>
            <average>86.96832275</average>
            <std>5.27337313</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">8.8</x>
            <y units="Å">8.8</y>
            <z units="Å">8.8</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>94.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Tomogram of stacked thylakoid membranes. Includes two dimensional crystal of photosystem II complexes in a grana membrane.</annotation_details>
        <details>::::EMDATABANK.org::::EMD-2384::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_2384.tif</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>
