<emd emdb_id="EMD-5270" 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>2011-03-24</deposition>
            <header_release>2011-06-23</header_release>
            <map_release>2011-06-27</map_release>
            <update>2011-09-23</update>
        </key_dates>
        <title>The entire ectodomain of bovine Nrx1alpha</title>
        <authors_list>
            <author>Tanaka H</author>
            <author>Nogi T</author>
            <author>Yasui N</author>
            <author>Iwasaki K</author>
            <author>Takagi J</author>
        </authors_list>
        <keywords>synapse, neulexin, neuroligin, single particle reconstruction</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Tanaka H</author>
                    <author order="2">Nogi T</author>
                    <author order="3">Yasui N</author>
                    <author order="4">Iwasaki K</author>
                    <author order="5">Takagi J</author>
                    <title>Structural basis for variant-specific neuroligin-binding by alpha-neurexin.</title>
                    <journal>PLOS ONE</journal>
                    <volume>6</volume>
                    <first_page>e19411</first_page>
                    <last_page>e19411</last_page>
                    <year>2011</year>
                    <external_references type="PUBMED">21552542</external_references>
                    <external_references type="DOI">doi:10.1371/journal.pone.0019411</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>an ectodomain  fragment of  alpha-neurexin 1</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>an ectodomain  fragment of  alpha-neurexin 1</name>
                <details>The sample was subjected to a size exclusion chromatography before negatively staining</details>
                <oligomeric_state>monomer</oligomeric_state>
                <number_unique_components>1</number_unique_components>
                <molecular_weight>
                    <experimental units="MDa">0.14</experimental>
                    <theoretical units="MDa">0.14</theoretical>
                    <method>SDS-PAGE</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="Neurexin">Neurexin</name>
                <natural_source database="NCBI">
                    <organism ncbi="32644">unidentified</organism>
                    <synonym_organism>bovine</synonym_organism>
                    <organelle>Synapse</organelle>
                    <cellular_location>Cell membrane</cellular_location>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">0.14</experimental>
                    <theoretical units="MDa">0.14</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <oligomeric_state>Monomer</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism>CHO Cells</recombinant_organism>
                    <recombinant_plasmid>pcDNA3.1</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="GO">GO:0007155</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">
                    <staining>
                        <type>NEGATIVE</type>
                        <details>2% w/v uranyl acetate</details>
                    </staining>
                    <vitrification>
                        <cryogen_name>NONE</cryogen_name>
                        <instrument>OTHER</instrument>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>HITACHI H-9500SD</microscope>
                    <illumination_mode>SPOT SCAN</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">300</acceleration_voltage>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">293</temperature_average>
                    </temperature>
                    <specimen_holder>Normal HITACHI side entry holder</specimen_holder>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <final_reconstruction>
                    <software_list>
                        <software>
                            <name>EMAN</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="31251">
        <file>emd_5270.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>200</col>
            <row>200</row>
            <sec>200</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-100</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>200</z>
        </spacing>
        <cell>
            <a units="&#8491;">440</a>
            <b units="&#8491;">440</b>
            <c units="&#8491;">440</c>
            <alpha units="deg">90</alpha>
            <beta units="deg">90</beta>
            <gamma units="deg">90</gamma>
        </cell>
        <axis_order>
            <fast>X</fast>
            <medium>Y</medium>
            <slow>Z</slow>
        </axis_order>
        <statistics>
            <minimum>-11.7317</minimum>
            <maximum>29.890899999999998</maximum>
            <average>-0.0000000071204</average>
            <std>1.0</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.2</x>
            <y units="&#8491;">2.2</y>
            <z units="&#8491;">2.2</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>7.59</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>This is a 3-D map of the entire ectodomain of bovine Nrx1alpha</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5270::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>3ASI</access_code>
                </initial_model>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>