<emd emdb_id="EMD-6482" 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>2015-10-14</deposition>
            <header_release>2015-11-25</header_release>
            <map_release>2015-12-16</map_release>
            <update>2016-02-17</update>
        </key_dates>
        <title>Cryo-electron microscopy of alpha Synuclein amyloid fibrils</title>
        <authors_list>
            <author>Dearborn AD</author>
            <author>Wall JS</author>
            <author>Cheng N</author>
            <author>Heymann JB</author>
            <author>Kajava AV</author>
            <author>Varkey J</author>
            <author>Langen R</author>
            <author>Steven AC</author>
        </authors_list>
        <keywords />
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Dearborn AD</author>
                    <author order="2">Wall JS</author>
                    <author order="3">Cheng N</author>
                    <author order="4">Heymann JB</author>
                    <author order="5">Kajava AV</author>
                    <author order="6">Varkey J</author>
                    <author order="7">Langen R</author>
                    <author order="8">Steven AC</author>
                    <title>alpha-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated, Protofibrils.</title>
                    <journal>J.BIOL.CHEM.</journal>
                    <volume>291</volume>
                    <first_page>2310</first_page>
                    <last_page>2318</last_page>
                    <year>2016</year>
                    <external_references type="PUBMED">26644467</external_references>
                    <external_references type="DOI">doi:10.1074/jbc.M115.698787</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>In vitro assembled, recombinant amyloid fibrils of full-length human alpha Synuclein</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>In vitro assembled, recombinant amyloid fibrils of full-length human alpha Synuclein</name>
                <details>The sample was morphologically heterogeneous.</details>
                <oligomeric_state>dimeric asymmetric unit</oligomeric_state>
                <number_unique_components>2</number_unique_components>
                <molecular_weight>
                    <method>Dark-field scanning transmission electron microscopy 59.1 MDa/micron compared to 61.5 MDa/micron theoretical weight</method>
                </molecular_weight>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="NACP, PARK1">alpha Synuclein</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <synonym_organism>Human</synonym_organism>
                    <tissue>Brain</tissue>
                    <cell>Neuron</cell>
                    <cellular_location>Lewy Body</cellular_location>
                </natural_source>
                <oligomeric_state>Amyloid</oligomeric_state>
                <recombinant_exp_flag>true</recombinant_exp_flag>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="469008">Escherichia coli BL21(DE3)</recombinant_organism>
                    <recombinant_strain>BL21*(DE3)pLysS</recombinant_strain>
                    <recombinant_plasmid>pRK172aS</recombinant_plasmid>
                </recombinant_expression>
                <sequence>
                    <external_references type="UNIPROTKB">P37840</external_references>
                    <external_references type="GO">GO:0000287</external_references>
                    <external_references type="GO">GO:0005504</external_references>
                    <external_references type="GO">GO:0005507</external_references>
                    <external_references type="GO">GO:0005509</external_references>
                    <external_references type="GO">GO:0005515</external_references>
                    <external_references type="INTERPRO">IPR002460</external_references>
                </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">
                    <concentration units="mg/mL">4</concentration>
                    <buffer>
                        <ph>7.4</ph>
                        <details>10 mM HEPES, 100 mM NaCl, 0.1% NaN3</details>
                    </buffer>
                    <grid>
                        <details>R1.2/1.3 400 mesh copper Quantifoil grid, glow-discharged in argon/oxygen</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">90</chamber_temperature>
                        <instrument>LEICA KF80</instrument>
                        <method>Manually blotted before plunging</method>
                    </vitrification>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI/PHILIPS CM200FEG</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">120</acceleration_voltage>
                    <nominal_cs units="mm">2.0</nominal_cs>
                    <nominal_defocus_min units="&#181;m">2.0</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">3.5</nominal_defocus_max>
                    <nominal_magnification>50000.0</nominal_magnification>
                    <calibrated_magnification>51840.0</calibrated_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <date>2012-06-05</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>NIKON SUPER COOLSCAN 9000</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>110</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <details>The 2D reconstructions were made and aligned using bhelcross. The helical parameters were determined per fibril in real space and imposed on the average using bhelcross.</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="&#8491;">4.7</delta_z>
                            <delta_phi units="deg">1.1</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <resolution res_type="BY AUTHOR" units="&#8491;">40.0</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>Bsoft</name>
                        </software>
                    </software_list>
                    <details>Extruded from a 2D reconstruction based upon helical parameters</details>
                </final_reconstruction>
                <ctf_correction>
                    <details>phase-flipped micrograph</details>
                </ctf_correction>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="15151">
        <file>emd_6482.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>80</col>
            <row>80</row>
            <sec>606</sec>
        </dimensions>
        <origin>
            <col>-40</col>
            <row>-40</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>80</x>
            <y>80</y>
            <z>606</z>
        </spacing>
        <cell>
            <a units="&#8491;">203.2</a>
            <b units="&#8491;">203.2</b>
            <c units="&#8491;">1539.24</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>-3.53419471</minimum>
            <maximum>8.32841015</maximum>
            <average>0.33484867</average>
            <std>2.09454417</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.54</x>
            <y units="&#8491;">2.54</y>
            <z units="&#8491;">2.54</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>3.66</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Extruded 2D reconstruction of in vitro assembled alpha Synuclein amyoid fibrils</annotation_details>
        <details>::::EMDATABANK.org::::EMD-6482::::</details>
    </map>
    <interpretation>
        <figure_list>
            <figure>
                <file>emd_6482.png</file>
            </figure>
        </figure_list>
    </interpretation>
</emd>