<emd emdb_id="EMD-5194" 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>2010-04-22</deposition>
            <header_release>2010-05-05</header_release>
            <map_release>2010-09-01</map_release>
            <update>2010-10-19</update>
        </key_dates>
        <title>Structural map of MT 14-3</title>
        <authors_list>
            <author>Sui H</author>
            <author>Downing KH</author>
        </authors_list>
        <keywords>microtubule, ultrastructure, Cryoelectron Microscopy Computer-Assisted Image Processing</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Sui H</author>
                    <author order="2">Downing KH</author>
                    <title>Structural basis of interprotofilament interaction and lateral deformation of microtubules.</title>
                    <journal>STRUCTURE</journal>
                    <volume>18</volume>
                    <first_page>1022</first_page>
                    <last_page>1031</last_page>
                    <year>2010</year>
                    <external_references type="PUBMED">20696402</external_references>
                    <external_references type="DOI">doi:10.1016/j.str.2010.05.010</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
    </crossreferences>
    <sample>
        <name>The microtubule containing 14 protofilaments</name>
        <supramolecule_list>
            <sample_supramolecule supramolecule_id="1000">
                <name>The microtubule containing 14 protofilaments</name>
                <oligomeric_state>The 14-protofilament microtubule forms a pseudo helix</oligomeric_state>
                <number_unique_components>2</number_unique_components>
            </sample_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name synonym="MT 14-3">microtubule with 14 protofilaments</name>
                <natural_source database="NCBI">
                    <organism ncbi="9913">Bos taurus</organism>
                    <synonym_organism>Bovine</synonym_organism>
                    <tissue>Brain</tissue>
                </natural_source>
                <molecular_weight>
                    <experimental units="MDa">50</experimental>
                    <theoretical units="MDa">50</theoretical>
                </molecular_weight>
                <details>Microtubule with 14 protofilaments and 3-start helical structure (pseudo-helix)</details>
                <oligomeric_state>Dimer</oligomeric_state>
                <recombinant_exp_flag>false</recombinant_exp_flag>
                <recombinant_expression database="NCBI" />
                <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">
                    <buffer>
                        <ph>6.8</ph>
                        <details>25mM Pipes, 25mM NaCl, 2mM MgCl2, 1mM EGTA</details>
                    </buffer>
                    <grid>
                        <details>300 mesh copper grid covered with home-made carbon films</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_temperature units="K">93</chamber_temperature>
                        <instrument>HOMEMADE PLUNGER</instrument>
                        <details>Vitrification instrument: Home made plunger</details>
                        <method>Blot for 2 second before plunging</method>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>JEOL 4000EX</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>LAB6</electron_source>
                    <acceleration_voltage units="kV">400</acceleration_voltage>
                    <nominal_cs units="mm">4.1</nominal_cs>
                    <nominal_defocus_min units="&#181;m">0.5</nominal_defocus_min>
                    <nominal_defocus_max units="&#181;m">2.0</nominal_defocus_max>
                    <nominal_magnification>60000.0</nominal_magnification>
                    <specimen_holder_model>GATAN LIQUID NITROGEN</specimen_holder_model>
                    <temperature>
                        <temperature_average units="K">105</temperature_average>
                    </temperature>
                    <alignment_procedure>
                        <legacy>
                            <astigmatism>Objective lens astigmatism was corrected at 400,000 times magnification</astigmatism>
                            <electron_beam_tilt_params>0</electron_beam_tilt_params>
                        </legacy>
                    </alignment_procedure>
                    <date>2007-07-12</date>
                    <image_recording_list>
                        <image_recording>
                            <film_or_detector_model category="FILM">KODAK SO-163 FILM</film_or_detector_model>
                            <digitization_details>
                                <scanner>OTHER</scanner>
                                <sampling_interval units="&#181;m">6.35</sampling_interval>
                            </digitization_details>
                            <number_real_images>425</number_real_images>
                            <average_electron_dose_per_image units="e/&#8491;^2">15</average_electron_dose_per_image>
                            <details>The micrographs were digitized with a customized robotic scanning system that uses a Nikon Coolpix 8000 scanner</details>
                            <bits_per_pixel>16.</bits_per_pixel>
                        </image_recording>
                    </image_recording_list>
                    <specimen_holder>Side entry liquid nitrogen-cooled cryo specimen holder</specimen_holder>
                    <tilt_angle_min>0</tilt_angle_min>
                    <tilt_angle_max>0</tilt_angle_max>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <details>With addition of Taxol or Taxotere for microtubule stabilization</details>
                <ctf_correction>
                    <details>Each micrograph</details>
                </ctf_correction>
                <final_reconstruction>
                    <resolution res_type="BY AUTHOR" units="&#8491;">9.3</resolution>
                    <resolution_method>OTHER</resolution_method>
                    <software_list>
                        <software>
                            <name>SPIDER</name>
                        </software>
                    </software_list>
                </final_reconstruction>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="18751">
        <file>emd_5194.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>120</sec>
        </dimensions>
        <origin>
            <col>-100</col>
            <row>-100</row>
            <sec>-100</sec>
        </origin>
        <spacing>
            <x>200</x>
            <y>200</y>
            <z>120</z>
        </spacing>
        <cell>
            <a units="&#8491;">406</a>
            <b units="&#8491;">406</b>
            <c units="&#8491;">243.6</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>-3.04762</minimum>
            <maximum>6.35733</maximum>
            <average>0.0010584</average>
            <std>0.91308</std>
        </statistics>
        <pixel_spacing>
            <x units="&#8491;">2.03</x>
            <y units="&#8491;">2.03</y>
            <z units="&#8491;">2.03</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>2.1</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <annotation_details>Structural maps of MT 14-3</annotation_details>
        <details>::::EMDATABANK.org::::EMD-5194::::</details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>1JFF</access_code>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <software_list>
                    <software>
                        <name>Chimera</name>
                    </software>
                </software_list>
                <details>Protocol: Rigid Body. A homology model was generated for the missing region in 1JFF from residues 35 to 60 in alpha-tubulin (by N. Banavali). The tubulin dimer structure was fitted into the density maps using the rigid body fitting function in Chimera</details>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>