<emd emdb_id="EMD-6425" 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>2015-08-12</deposition>
            <header_release>2015-09-23</header_release>
            <map_release>2016-04-27</map_release>
            <update>2016-06-08</update>
        </key_dates>
        <title>Retinoschisin, back-to-back octameric rings</title>
        <authors_list>
            <author>Heymann JB</author>
            <author>Tolun G</author>
            <author>Vijayasarathy C</author>
            <author>Huang R</author>
            <author>Zeng Y</author>
            <author>Li Y</author>
            <author>Steven AC</author>
            <author>Sieving PA</author>
        </authors_list>
        <keywords>X-linked retinoschisis, discoidin domain, retina, macular degeneration, vision</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Tolun G</author>
                    <author order="2">Vijayasarathy C</author>
                    <author order="3">Huang R</author>
                    <author order="4">Zeng Y</author>
                    <author order="5">Li Y</author>
                    <author order="6">Steven AC</author>
                    <author order="7">Sieving PA</author>
                    <author order="8">Heymann JB</author>
                    <title>Paired octamer rings of retinoschisin suggest a junctional model for cell-cell adhesion in the retina.</title>
                    <journal>PROC.NAT.ACAD.SCI.USA</journal>
                    <volume>113</volume>
                    <first_page>5287</first_page>
                    <last_page>5292</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">27114531</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1519048113</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>3jd6</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>Mature retinoschisin with a C-terminal hexahistidine tag</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>Mature retinoschisin with a C-terminal hexahistidine tag</name>
                <oligomeric_state>16-mer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.4</experimental>
                    <theoretical units="MDa">0.382</theoretical>
                    <method>Blue native gel electrophoresis</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="RS1">Retinoschisin 1</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <tissue>Retina</tissue>
                    <cell>Photoreceptors and bipolar cells</cell>
                    <organelle>Extracellular space</organelle>
                    <cellular_location>Forming a junction between cells</cellular_location>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.024</theoretical>
                </molecular_weight>
                <details>The mature RS1 protein (no signal sequence) with a C-terminal six-histidine tag</details>
                <number_of_copies>16</number_of_copies>
                <oligomeric_state>16-mer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="7108">Spodoptera frugiperda</recombinant_organism>
                    <recombinant_cell>Sf9</recombinant_cell>
                    <recombinant_plasmid>pDonr253</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">O15537</external_references>
                </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">
                    <concentration units="mg/mL">0.2</concentration>
                    <buffer>
                        <ph>7.5</ph>
                        <details>20 mM Tris-HCl, 150 mM NaCl</details>
                    </buffer>
                    <grid>
                        <details>C-flat holey carbon grids (2.0 um holes, 2.0 um spaces)</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <instrument>LEICA EM GP</instrument>
                        <details>Plunged at room temperature.</details>
                        <method>Blotted from the copper side.</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_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">2.0</nominal_cs>
                    <nominal_magnification>39000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <date>2014-06-11</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="CCD">GATAN K2 (4k x 4k)</film_or_detector_model>
                            <digitization_details>
                                <sampling_interval units="&#181;m">5</sampling_interval>
                            </digitization_details>
                            <number_real_images>19</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">30</average_electron_dose_per_image>
                            <details>Each image is the average of 10 frames taken over 3 seconds.</details>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>Particles were picked semi-automatically (EMAN2).</details>
                <ctf_correction>
                    <details>Each particle</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">4.1</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Relion, EMAN2, Bsoft</name>
                        </software>
                    </software_list>
                    <number_images_used>9096</number_images_used>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="16001">
        <file>emd_6425.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>160</col>
            <row>160</row>
            <sec>160</sec>
        </dimensions>
        <origin>
            <col>-80</col>
            <row>-80</row>
            <sec>-80</sec>
        </origin>
        <spacing>
            <x>160</x>
            <y>160</y>
            <z>160</z>
        </spacing>
        <cell>
            <a units="&#8491;">164.79999</a>
            <b units="&#8491;">164.79999</b>
            <c units="&#8491;">164.79999</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>-3.07950211</minimum>
            <maximum>6.21566534</maximum>
            <average>0.0</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">1.03</x>
            <y units="&#8491;">1.03</y>
            <z units="&#8491;">1.03</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.0</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Retinoschisin double octamer rings</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6425::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1SDD</access_code>
                </initial_model>
                <refinement_protocol>FLEXIBLE FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>COOT, MDFF, Foldit</name>
                    </software>
                </software_list>
                <details>Flexible fitting</details>
                <target_criteria>FSC(0.5) = 4.7</target_criteria>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <figure_list>
            <figure>
                <file>emd_6425.png</file>
            </figure>
        </figure_list>
    </interpretation>
    <validation>
        <fsc_curve>
            <file>emd_6425_fsc.xml</file>
        </fsc_curve>
    </validation>
</emd>