<?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_1/emdb.xsd" version="3.0.9.1" emdb_id="EMD-27220">
    <admin>
        <current_status>
            <date>2024-02-07</date>
            <code>OBS</code>
            <processing_site>RCSB</processing_site>
        </current_status>
        <sites>
            <deposition>RCSB</deposition>
            <last_processing>RCSB</last_processing>
        </sites>
        <key_dates>
            <deposition>2022-06-06</deposition>
            <header_release>2022-11-23</header_release>
            <map_release>2022-11-23</map_release>
            <obsolete>2024-02-07</obsolete>
            <update>2024-02-07</update>
        </key_dates>
        <grant_support>
            <grant_reference>
                <funding_body>National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)</funding_body>
                <code>R35GM137957</code>
                <country>United States</country>
            </grant_reference>
        </grant_support>
        <title>ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation</title>
        <authors_list>
            <author>Petroff II JT</author>
            <author>Deng Z</author>
            <author>Rau MJ</author>
            <author>Fitzpatrick JAJ</author>
            <author>Yuan P</author>
            <author>Cheng WWL</author>
        </authors_list>
        <keywords>ELIC, ion channel, pLGIC, STRUCTURAL PROTEIN</keywords>
    </admin>
    <crossreferences>
        <citation_list>
            <primary_citation>
                <journal_citation published="true">
                    <author order="1">Petroff II JT</author>
                    <author order="2">Dietzen NM</author>
                    <author ORCID="0000-0002-0930-8277" order="3">Santiago-McRae E</author>
                    <author order="4">Deng B</author>
                    <author order="5">Washington MS</author>
                    <author order="6">Chen LJ</author>
                    <author ORCID="0000-0002-8996-832X" order="7">Trent Moreland K</author>
                    <author order="8">Deng Z</author>
                    <author ORCID="0000-0001-5170-2000" order="9">Rau M</author>
                    <author ORCID="0000-0002-7907-3602" order="10">Fitzpatrick JAJ</author>
                    <author ORCID="0000-0002-5660-225X" order="11">Yuan P</author>
                    <author ORCID="0000-0003-1323-3244" order="12">Joseph TT</author>
                    <author ORCID="0000-0003-2540-4098" order="13">Henin J</author>
                    <author ORCID="0000-0001-8949-2694" order="14">Brannigan G</author>
                    <author ORCID="0000-0002-9529-9820" order="15">Cheng WWL</author>
                    <title>Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation.</title>
                    <journal_abbreviation>Nat Commun</journal_abbreviation>
                    <country>UK</country>
                    <volume>13</volume>
                    <first_page>7017</first_page>
                    <last_page>7017</last_page>
                    <year>2022</year>
                    <external_references type="PUBMED">36385237</external_references>
                    <external_references type="DOI">doi:10.1038/s41467-022-34813-5</external_references>
                    <external_references type="ISSN">2041-1723</external_references>
                </journal_citation>
            </primary_citation>
        </citation_list>
        <emdb_list>
            <emdb_reference>
                <emdb_id>EMD-27219</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-27218</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-27217</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-27216</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
            <emdb_reference>
                <emdb_id>EMD-27215</emdb_id>
                <relationship>
                    <other>other EM volume</other>
                </relationship>
            </emdb_reference>
        </emdb_list>
        <pdb_list>
            <pdb_reference>
                <pdb_id>8d68</pdb_id>
                <relationship>
                    <in_frame>FULLOVERLAP</in_frame>
                </relationship>
            </pdb_reference>
        </pdb_list>
    </crossreferences>
    <sample>
        <name>ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc</name>
        <supramolecule_list>
            <complex_supramolecule supramolecule_id="1">
                <name>ELIC5 (P254G/C300S/V261Y/G319F/I320F) with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc</name>
                <parent>0</parent>
                <macromolecule_list>
                    <macromolecule>
                        <macromolecule_id>1</macromolecule_id>
                    </macromolecule>
                </macromolecule_list>
                <natural_source database="NCBI">
                    <organism ncbi="204038">Dickeya dadantii</organism>
                </natural_source>
            </complex_supramolecule>
        </supramolecule_list>
        <macromolecule_list>
            <protein_or_peptide macromolecule_id="1">
                <name>Erwinia ligand-gated ion channel</name>
                <natural_source database="NCBI">
                    <organism ncbi="204038">Dickeya dadantii</organism>
                </natural_source>
                <molecular_weight>
                    <theoretical units="MDa">0.037011055</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <recombinant_expression database="NCBI">
                    <recombinant_organism ncbi="562">Escherichia coli</recombinant_organism>
                </recombinant_expression>
                <enantiomer>LEVO</enantiomer>
                <sequence>
                    <string>APADNAADARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFIN
VVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEW
WIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTLML
TVVAYAFYTSNILGRLPYTTYIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRSRLAFPLGFLAIGCVLVIRFF
TL</string>
                    <external_references type="UNIPROTKB">E0SJQ4</external_references>
                </sequence>
            </protein_or_peptide>
            <ligand macromolecule_id="2">
                <name>(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate</name>
                <molecular_weight>
                    <theoretical units="MDa">0.0007490069999999999</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <formula>PGW</formula>
            </ligand>
            <ligand macromolecule_id="3">
                <name>2-AMINO-ETHANETHIOL</name>
                <molecular_weight>
                    <theoretical units="MDa">7.7149e-05</theoretical>
                </molecular_weight>
                <number_of_copies>5</number_of_copies>
                <formula>DHL</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">
                    <buffer>
                        <ph>7.5</ph>
                    </buffer>
                    <grid>
                        <model>Quantifoil R2/2</model>
                        <material>COPPER</material>
                        <mesh>300</mesh>
                        <pretreatment>
                            <type>PLASMA CLEANING</type>
                            <time units="s">60</time>
                            <atmosphere>OTHER</atmosphere>
                            <pressure units="kPa">9.332</pressure>
                        </pretreatment>
                        <details>H2 27.5 sccm
O2 6.4 sccm</details>
                    </grid>
                    <vitrification>
                        <cryogen_name>ETHANE</cryogen_name>
                        <chamber_humidity units="percentage">100</chamber_humidity>
                        <chamber_temperature units="K">277</chamber_temperature>
                        <instrument>FEI VITROBOT MARK IV</instrument>
                        <details>Blot for 2 seconds before plunging. </details>
                    </vitrification>
                </single_particle_preparation>
            </specimen_preparation_list>
            <microscopy_list>
                <single_particle_microscopy microscopy_id="1">
                    <microscope>FEI TITAN KRIOS</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">150.0</c2_aperture_diameter>
                    <nominal_cs units="mm">0.01</nominal_cs>
                    <nominal_defocus_min units="µm">1.0</nominal_defocus_min>
                    <calibrated_defocus_min units="µm">1.0</calibrated_defocus_min>
                    <nominal_defocus_max units="µm">2.5</nominal_defocus_max>
                    <calibrated_defocus_max units="µm">2.5</calibrated_defocus_max>
                    <nominal_magnification>105000.0</nominal_magnification>
                    <calibrated_magnification>105000.0</calibrated_magnification>
                    <specimen_holder_model>FEI TITAN KRIOS AUTOGRID HOLDER</specimen_holder_model>
                    <cooling_holder_cryogen>NITROGEN</cooling_holder_cryogen>
                    <temperature>
                        <temperature_min units="K">82.0</temperature_min>
                        <temperature_max units="K">84.0</temperature_max>
                    </temperature>
                    <alignment_procedure>
                        <zemlin_tableau/>
                    </alignment_procedure>
                    <specialist_optics>
                        <sph_aberration_corrector>Microscope was equipped with a Cs corrector</sph_aberration_corrector>
                        <energy_filter>
                            <name>GIF Bioquantum</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>COUNTING</detector_mode>
                            <digitization_details>
                                <dimensions>
                                    <width units="pixel">3838</width>
                                    <height units="pixel">3710</height>
                                </dimensions>
                            </digitization_details>
                            <number_grids_imaged>1</number_grids_imaged>
                            <average_exposure_time units="s">8.0</average_exposure_time>
                            <average_electron_dose_per_image units="e/Å^2">1.65</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>
                <startup_model type_of_model="INSILICO MODEL"/>
                <final_reconstruction>
                    <resolution units="Å" res_type="BY AUTHOR">3.36</resolution>
                    <resolution_method>FSC 0.143 CUT-OFF</resolution_method>
                    <number_images_used>195134</number_images_used>
                </final_reconstruction>
                <initial_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                </initial_angle_assignment>
                <final_angle_assignment>
                    <type>ANGULAR RECONSTITUTION</type>
                </final_angle_assignment>
            </singleparticle_processing>
        </structure_determination>
    </structure_determination_list>
    <map format="CCP4" size_kbytes="23329">
        <file>emd_27220.map.gz</file>
        <symmetry>
            <space_group>1</space_group>
        </symmetry>
        <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
        <dimensions>
            <col>180</col>
            <row>180</row>
            <sec>180</sec>
        </dimensions>
        <origin>
            <col>0</col>
            <row>0</row>
            <sec>0</sec>
        </origin>
        <spacing>
            <x>180</x>
            <y>180</y>
            <z>180</z>
        </spacing>
        <cell>
            <a units="Å">208.79999</a>
            <b units="Å">208.79999</b>
            <c units="Å">208.79999</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>-0.39578897</minimum>
            <maximum>0.65561306</maximum>
            <average>0.0015338252</average>
            <std>0.025711367</std>
        </statistics>
        <pixel_spacing>
            <x units="Å">1.16</x>
            <y units="Å">1.16</y>
            <z units="Å">1.16</z>
        </pixel_spacing>
        <contour_list>
            <contour primary="true">
                <level>0.0855</level>
                <source>AUTHOR</source>
            </contour>
        </contour_list>
        <label>::::EMDATABANK.org::::EMD-27220::::</label>
    </map>
    <interpretation>
        <modelling_list>
            <modelling>
                <initial_model>
                    <access_code>2YN6</access_code>
                    <chain>
                        <source_name>PDB</source_name>
                        <initial_model_type>experimental model</initial_model_type>
                    </chain>
                </initial_model>
                <refinement_protocol>AB INITIO MODEL</refinement_protocol>
                <refinement_space>REAL</refinement_space>
            </modelling>
        </modelling_list>
        <additional_map_list>
            <additional_map format="CCP4" size_kbytes="23329">
                <file>emd_27220_additional_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>180</col>
                    <row>180</row>
                    <sec>180</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>180</x>
                    <y>180</y>
                    <z>180</z>
                </spacing>
                <cell>
                    <a units="Å">208.79999</a>
                    <b units="Å">208.79999</b>
                    <c units="Å">208.79999</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>-0.03410931</minimum>
                    <maximum>0.13339941</maximum>
                    <average>0.0006792439</average>
                    <std>0.008264159</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.16</x>
                    <y units="Å">1.16</y>
                    <z units="Å">1.16</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-27220::::</label>
            </additional_map>
        </additional_map_list>
        <half_map_list>
            <half_map format="CCP4" size_kbytes="23329">
                <file>emd_27220_half_map_2.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>180</col>
                    <row>180</row>
                    <sec>180</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>180</x>
                    <y>180</y>
                    <z>180</z>
                </spacing>
                <cell>
                    <a units="Å">208.79999</a>
                    <b units="Å">208.79999</b>
                    <c units="Å">208.79999</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>-0.04840773</minimum>
                    <maximum>0.14261544</maximum>
                    <average>0.000676595</average>
                    <std>0.008724114</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.16</x>
                    <y units="Å">1.16</y>
                    <z units="Å">1.16</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-27220::::</label>
            </half_map>
            <half_map format="CCP4" size_kbytes="23329">
                <file>emd_27220_half_map_1.map.gz</file>
                <symmetry>
                    <space_group>1</space_group>
                </symmetry>
                <data_type>IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)</data_type>
                <dimensions>
                    <col>180</col>
                    <row>180</row>
                    <sec>180</sec>
                </dimensions>
                <origin>
                    <col>0</col>
                    <row>0</row>
                    <sec>0</sec>
                </origin>
                <spacing>
                    <x>180</x>
                    <y>180</y>
                    <z>180</z>
                </spacing>
                <cell>
                    <a units="Å">208.79999</a>
                    <b units="Å">208.79999</b>
                    <c units="Å">208.79999</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>-0.040096752</minimum>
                    <maximum>0.14558512</maximum>
                    <average>0.0006820838</average>
                    <std>0.008721599</std>
                </statistics>
                <pixel_spacing>
                    <x units="Å">1.16</x>
                    <y units="Å">1.16</y>
                    <z units="Å">1.16</z>
                </pixel_spacing>
                <contour_list>
                    <contour primary="true">
                        <source>AUTHOR</source>
                    </contour>
                </contour_list>
                <label>::::EMDATABANK.org::::EMD-27220::::</label>
            </half_map>
        </half_map_list>
    </interpretation>
</emd>
