<?xml version="1.0" encoding="UTF-8"?>
<emd xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://ftp.ebi.ac.uk/pub/databases/em_ebi/emdb_related/emdb-schemas/emdb_schemas/v3/v3_0_9_3/emdb.xsd" version="3.0.9.3" emdb_id="EMD-4400">
    <admin>
        <current_status>
            <date>2024-11-13</date>
            <code>REL</code>
            <processing_site>PDBe</processing_site>
        </current_status>
        <sites>
            <deposition>PDBe</deposition>
            <last_processing>PDBe</last_processing>
        </sites>
        <key_dates>
            <deposition>2018-11-01</deposition>
            <header_release>2018-11-14</header_release>
            <map_release>2018-12-19</map_release>
            <update>2024-11-13</update>
        </key_dates>
        <title>CryoEM reconstruction of full-length, fully-glycosylated human butyrylcholinesterase tetramer</title>
        <authors_list>
            <author>Leung MR</author>
            <author>van Bezouwen LS</author>
        </authors_list>
        <keywords>cholinesterase, tetramer, HYDROLASE</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Leung MR</author>
                    <author order="2">van Bezouwen LS</author>
                    <author order="3">Schopfer LM</author>
                    <author order="4">Sussman JL</author>
                    <author order="5">Silman I</author>
                    <author order="6">Lockridge O</author>
                    <author order="7">Zeev-Ben-Mordehai T</author>
                    <title>Cryo-EM structure of the native butyrylcholinesterase tetramer reveals a dimer of dimers stabilized by a superhelical assembly.</title>
                    <journal_abbreviation>Proc. Natl. Acad. Sci. U.S.A.</journal_abbreviation>
                    <country>US</country>
                    <volume>115</volume>
                    <first_page>13270</first_page>
                    <last_page>13275</last_page>
                    <year>2018</year>
                    <external_references type="PUBMED">30538207</external_references>
                    <external_references type="DOI">doi:10.1073/pnas.1817009115</external_references>
                    <external_references type="ISSN">1091-6490</external_references>
                    <external_references type="CSD">0040</external_references>
                    <external_references type="ASTM">PNASA6</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>6i2t</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>heteropentameric complex consisting of four copies of butyrylcholinesterase and one copy of a lamellipodin-derived polyproline peptide</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>heteropentameric complex consisting of four copies of butyrylcholinesterase and one copy of a lamellipodin-derived polyproline peptide</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                    <macromolecule>
                        <macromolecule_id>2</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                    <tissue>plasma</tissue>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.34</theoretical>
                </molecular_weight>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Cholinesterase</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.0651495</theoretical>
                </molecular_weight>
                <number_of_copies>4</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>EDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSE
MWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNP
EAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEAR
NRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVG
VNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFIC
PALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNP
NETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKVLEMTGNIDEAEWEWKAGFHRWNNYMMDWKNQ
FNDYTSKKESCVGL</string>
                    <external_references type="UNIPROTKB">P06276</external_references>
                </sequence>
                <ec_number>3.1.1.8</ec_number>
            </protein_or_peptide>
            <protein_or_peptide macromolecule_id="2">
                <name>lamellipodin-derived polyproline peptide</name>
                <natural_source database="NCBI">
                    <organism ncbi="9606">Homo sapiens</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.001183393</theoretical>
                </molecular_weight>
                <number_of_copies>1</number_of_copies>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>PPPPPPPPPPPP</string>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="3">
                <name>2-acetamido-2-deoxy-beta-D-glucopyranose</name>
                <molecular_weight>
                    <theoretical units="MDa">0.000221208</theoretical>
                </molecular_weight>
                <number_of_copies>8</number_of_copies>
                <formula>NAG</formula>
            </ligand>
        </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">3.3</concentration>
                    <buffer>
                        <ph>8.0</ph>
                        <component>
                            <concentration units="mM">10.0</concentration>
                            <formula>C4H11NO3</formula>
                            <name>Tris</name>
                        </component>
                    </buffer>
                    <grid>
                        <model>Quantifoil R1.2/1.3</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <support_film film_type_id="1">
                            <film_material>CARBON</film_material>
                            <film_topology>HOLEY</film_topology>
                        </support_film>
                        <pretreatment>
                            <type>GLOW DISCHARGE</type>
                            <time units="s">30</time>
                        </pretreatment>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">90</chamber_humidity>
                        <chamber_temperature units="K">293</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>blot for either 2s or 3s at blot force -2 or 0, respectively. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TALOS ARCTICA</microscope>
                    <illumination_mode>FLOOD BEAM</illumination_mode>
                    <imaging_mode>BRIGHT FIELD</imaging_mode>
                    <electron_source>FIELD EMISSION GUN</electron_source>
                    <acceleration_voltage units="kV">200</acceleration_voltage>
                    <c2_aperture_diameter units="µm">50.0</c2_aperture_diameter>
                    <nominal_cs units="mm">2.7</nominal_cs>
                    <nominal_defocus_min units="µm">1.2</nominal_defocus_min>
                    <nominal_defocus_max units="µm">2.5</nominal_defocus_max>
                    <nominal_magnification>130000.0</nominal_magnification>
                    <specimen_holder_model>OTHER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <specialist_optics>
                        <energy_filter>
                            <name>GIF Quantum LS</name>
                            <slit_width units="eV">20</slit_width>
                        </energy_filter>
                    </specialist_optics>
                    <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>SUPER-RESOLUTION</detector_mode>
                            <number_grids_imaged>2</number_grids_imaged>
                            <number_real_images>4518</number_real_images>
                            <average_exposure_time units="s">6.3</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">49.5</average_electron_dose_per_image>
                        </image_recording>
                    </image_recording_list>
                </single_particle_microscopy>
            </microscopy_list>
            <singleparticle_processing image_processing_id="1">
                <image_recording_id>1</image_recording_id>
                <particle_selection>
                    <number_selected>414189</number_selected>
                </particle_selection>
                <startup_model type_of_model="NONE"/>
                <final_reconstruction>
                    <number_classes_used>1</number_classes_used>
                    <applied_symmetry>
                        <point_group>C2</point_group>
                    </applied_symmetry>
                    <resolution units="Å" res_type="BY AUTHOR">5.7</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                    <number_images_used>111986</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>MAXIMUM LIKELIHOOD</type>
                    <software_list>
                        <software>
                            <name>RELION</name>
                        </software>
                    </software_list>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="108001">
        <file>emd_4400.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>300</col>
            <row>300</row>
            <sec>300</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>300</x>
            <y>300</y>
            <z>300</z>
        </spacing>
        <cell>
            <a units="Å">308.55</a>
            <b units="Å">308.55</b>
            <c units="Å">308.55</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>-0.03921342</minimum>
            <maximum>0.0840524</maximum>
            <average>0.0002668748</average>
            <std>0.0023981098</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.0285</x>
            <y units="Å">1.0285</y>
            <z units="Å">1.0285</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.018</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-4400::::</label>
        <annotation_details>cryo-EM map of tetrameric full-length, glycosylated human butyrylcholinesterase (HuBChE) purified from human plasma</annotation_details>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>4AQD</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <initial_model>
                    <access_code>1VZJ</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>RIGID BODY FIT</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
    </interpretation>
</emd>
