<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://github.com/emdb-empiar/emdb-schemas/blob/master/v3/v3_0_1_4/emdb.xsd" emdb_id="EMD-7523" version="3.0.1.4">
    <admin>
        <current_status>
            <date>2019-05-15</date>
            <code>REL</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-03-06</deposition>
            <header_release>2018-04-11</header_release>
            <map_release>2019-01-16</map_release>
            <update>2019-05-15</update>
        </key_dates>
        <title>cryo-EM reconstruction of microtubule-bound 4R-tau</title>
        <authors_list>
            <author>Nogales E</author>
            <author>Hejab NMA</author>
            <author>Kellogg EH</author>
        </authors_list>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Kellogg EH</author>
                    <author order="2">Hejab NMA</author>
                    <author order="3">Poepsel S</author>
                    <author order="4">Downing KH</author>
                    <author order="5">DiMaio F</author>
                    <author order="6">Nogales E</author>
                    <title>Near-atomic model of microtubule-tau interactions.</title>
                    <journal_abbreviation>Science</journal_abbreviation>
                    <country>US</country>
                    <volume>360</volume>
                    <first_page>1242</first_page>
                    <last_page>1246</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">29748322</external_references>
                    <external_references type="DOI">doi:10.1126/science.aat1780</external_references>
                    <external_references type="ISSN">1095-9203</external_references>
                    <external_references type="CSD">0038</external_references>
                    <external_references type="ASTM">SCIEAS</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-7520</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>shortened tau (2R) construct</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-7522</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
                <details>full-length tau</details>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-7523</emdb_id>
                <relationship>
                    <other>associated EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
    </crossreferences>
    <sample>
        <name>Ternary complex of alpha-beta tubulin with shortened tau construct</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>Ternary complex of alpha-beta tubulin with shortened tau construct</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>3</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <details>Tau construct contains first four microtubule-targeting repeat motifs and portions of projection-domain and R' sequences</details>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>4Rtau</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>YSSPGSPGTPGSRSRTPSLPTPPTREPKKVAVVRTPPKSPSSAKSRLQTAPVPMPDLKNVKSKIGSTENLKHQPGGGKVQIINKKLDLSNVQSKCGSKDNIKHVPGGGSVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVEVKSEKLDFKDRVQSKIGSLDNITHVPGGGNKKIETHKLTFRENAKAKTDHGAEIVYKSPVVS</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>alpha-tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                </natural_source>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS</string>
                </sequence>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="3">
                <name>beta-tubulin</name>
                <natural_source database="NCBI">
                    <organism ncbi="9823">Sus scrofa</organism>
                </natural_source>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD</string>
                </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">0.5</concentration>
                    <buffer>
                        <ph>6.8</ph>
                        <component>
                            <concentration units="mM">80.0</concentration>
                            <formula>C8H18N2O6S2</formula>
                            <name>PIPES</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>C14H24N2O10</formula>
                            <name>EGTA</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>MgCl2</formula>
                            <name>Magnesium Chloride</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>C4H10O2S2</formula>
                            <name>DTT</name>
                        </component>
                        <component>
                            <concentration units="mM">1.0</concentration>
                            <formula>GTP</formula>
                            <name>Guanine tri-phosphate</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>C-flat-1.2/1.3 4C</model>
                        <material>COPPER</material>
                        <mesh>400</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <atmosphere>AIR</atmosphere>
                        </pretreatment>
                        <details>unspecified</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">310.15</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>blot force 10 pN, 6 second blot time. used C-flat 1.2/1.3 holey grids.
First 2 uL of microtubules were adhered to grid for 30 seconds, followed by 2 4 uL washes with 30 second incubation for each wash.. </details>
                    </vitrification>
                    <details>tubulin concentration is 0.5 mg/mL, tau concentration is 1 mg/mL</details>
                </helical_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <helical_microscopy microscopy_id="1">
                    <microscope>FEI TITAN</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>
                    <c2_aperture_diameter units="µm">100.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.5</nominal_defocus_max>
                    <nominal_magnification>27500.</nominal_magnification>
                    <specimen_holder_model>GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <alignment_procedure>
                        <coma_free/>
                    </alignment_procedure>
                    <image_recording_list>
                        <image_recording image_recording_id="1">
                            <film_or_detector_model>GATAN K2 SUMMIT (4k x 4k)</film_or_detector_model>
                            <detector_mode>COUNTING</detector_mode>
                            <digitization_details/>
                            <number_grids_imaged>1</number_grids_imaged>
                            <number_real_images>422</number_real_images>
                            <average_exposure_time units="s">6.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">27.5</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </helical_microscopy>
            </microscopy_list>
            <helical_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <details>used motioncorr to correct for beam-induced motion</details>
                <final_reconstruction>
                    <applied_symmetry>
                        <helical_parameters>
                            <delta_z units="Å">8.6</delta_z>
                            <delta_phi units="deg">-25.76</delta_phi>
                            <axial_symmetry>C1</axial_symmetry>
                        </helical_parameters>
                    </applied_symmetry>
                    <algorithm>FOURIER SPACE</algorithm>
                    <resolution units="Å" res_type="BY AUTHOR">4.8</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>FREALIGN</name>
                            <version>9.09</version>
                        </software>
                    </software_list>
                    <number_images_used>24618</number_images_used>
                </final_reconstruction>
                <ctf_correction>
                    <software_list>
                        <software>
                            <name>CTFFIND</name>
                            <version>4</version>
                        </software>
                    </software_list>
                </ctf_correction>
                <segment_selection>
                    <number_selected>36777</number_selected>
                    <software_list>
                        <software>
                            <name>Appion</name>
                        </software>
                    </software_list>
                    <details>manually selected helical segments, then filled in with overlapping boxes spaced 80 Angstrom apart.</details>
                </segment_selection>
                <startup_model type_of_model="EMDB MAP">
                    <emdb_id>EMD-5194</emdb_id>
                    <details>used a naked microtubule reconstruction as the initial model, low pass filtered to 20 Angstrom</details>
                </startup_model>
                <final_angle_assignment>
                    <type>NOT APPLICABLE</type>
                    <software_list>
                        <software>
                            <name>FREALIGN</name>
                            <version>9.09</version>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </helical_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="536871">
        <file>emd_7523.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>512</col>
            <row>512</row>
            <sec>512</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>512</x>
            <y>512</y>
            <z>512</z>
        </spacing>
        <cell>
            <a units="Å">675.84</a>
            <b units="Å">675.84</b>
            <c units="Å">675.84</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>-4.5460367</minimum>
            <maximum>14.269829</maximum>
            <average>0.059864923</average>
            <std>1.0374875</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.32</x>
            <y units="Å">1.32</y>
            <z units="Å">1.32</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>4.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-7523::::</label>
        <annotation_details>cryo-EM reconstruction of shortened tau construct (residues 197-400 of full-length tau)</annotation_details>
    </map>
</emd>
