[English] 日本語
Yorodumi
- PDB-6hy7: Crystal structure of alpha9 nAChR extracellular domain in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hy7
TitleCrystal structure of alpha9 nAChR extracellular domain in complex with alpha-conotoxin RgIA
Components
  • Alpha-conotoxin RgIA
  • Neuronal acetylcholine receptor subunit alpha-9
KeywordsTOXIN / alpha9 / ion channel / nAChR / acetylcholine / conotoxin / RgIA / antagonist
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / response to auditory stimulus / acetylcholine-gated channel complex / detection of mechanical stimulus involved in sensory perception of sound / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / inner ear morphogenesis ...Acetylcholine inhibits contraction of outer hair cells / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / response to auditory stimulus / acetylcholine-gated channel complex / detection of mechanical stimulus involved in sensory perception of sound / host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / ion channel regulator activity / inner ear morphogenesis / membrane depolarization / calcium channel activity / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / toxin activity / postsynaptic membrane / neuron projection / synapse / extracellular region / plasma membrane
Similarity search - Function
Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-conotoxin RgIA / Neuronal acetylcholine receptor subunit alpha-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Conus regius (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsGiastas, P. / Zouridakis, M.
CitationJournal: Front Pharmacol / Year: 2019
Title: Crystal Structure of the Monomeric Extracellular Domain of alpha 9 Nicotinic Receptor Subunit in Complex With alpha-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to alpha 9 ...Title: Crystal Structure of the Monomeric Extracellular Domain of alpha 9 Nicotinic Receptor Subunit in Complex With alpha-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to alpha 9 alpha 10 Nicotinic Receptors.
Authors: Zouridakis, M. / Papakyriakou, A. / Ivanov, I.A. / Kasheverov, I.E. / Tsetlin, V. / Tzartos, S. / Giastas, P.
History
DepositionOct 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-9
B: Alpha-conotoxin RgIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3895
Polymers26,8852
Non-polymers5043
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Functional inhibition of alpha9-containing nAChRs upon alpha-conotoxin RgIA addition
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint9 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.646, 82.530, 49.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Neuronal acetylcholine receptor subunit alpha-9 / Nicotinic acetylcholine receptor subunit alpha-9 / NACHR alpha-9


Mass: 25307.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: alpha9 nAChR / Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA9, NACHRA9 / Plasmid: pPicZa / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q9UGM1
#2: Protein/peptide Alpha-conotoxin RgIA


Mass: 1577.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: alpha conotoxin RgIA / Source: (synth.) Conus regius (invertebrata) / References: UniProt: P0C1D0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30% PEG 10000, 100mM Hepes

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→42.434 Å / Num. obs: 12622 / % possible obs: 98.87 % / Redundancy: 5.26 % / Net I/σ(I): 1.19
Reflection shellResolution: 2.26→2.36 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UXU

4uxu


Resolution: 2.26→42.434 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 31.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1175 5.04 %
Rwork0.1932 --
obs0.1962 23319 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→42.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 4 50 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091907
X-RAY DIFFRACTIONf_angle_d1.0532605
X-RAY DIFFRACTIONf_dihedral_angle_d12.9791125
X-RAY DIFFRACTIONf_chiral_restr0.057285
X-RAY DIFFRACTIONf_plane_restr0.006338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2597-2.36250.42471370.33672574X-RAY DIFFRACTION92
2.3625-2.48710.38151490.30452773X-RAY DIFFRACTION100
2.4871-2.64290.30361440.25792784X-RAY DIFFRACTION100
2.6429-2.84690.24591540.2242796X-RAY DIFFRACTION100
2.8469-3.13330.29431500.21582796X-RAY DIFFRACTION100
3.1333-3.58650.26851470.18792819X-RAY DIFFRACTION100
3.5865-4.51780.19961460.15852803X-RAY DIFFRACTION100
4.5178-42.4410.21551480.16292799X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52280.4832-0.26780.4617-0.31970.2898-0.0316-0.2325-0.12150.69590.06420.21770.2956-0.2096-0.01570.46240.0563-0.07480.3860.10410.350567.609813.235773.0118
20.6982-0.05060.23081.6279-0.27720.2650.1131-0.0687-0.1707-0.2150.071-0.23950.31950.14970.00010.3470.05180.03750.3121-0.03040.337273.743620.466757.9758
3-0.03060.05250.06971.1551-0.07340.8268-0.11480.0098-0.0038-0.16010.0595-0.21420.1856-0.037-0.00010.30510.01660.04480.3302-0.02570.336770.816727.660450.6058
40.52150.07710.68430.4837-0.69811.6917-0.01560.11310.1431-0.14350.0218-0.160.18250.2015-00.2666-0.00930.05090.2943-0.02080.34575.223734.092546.8283
50.1359-0.01150.118-0.00050.01970.0776-0.3296-0.44190.7194-0.3803-0.02460.9025-0.71060.79310.00020.6669-0.0507-0.1110.4466-0.05580.64150.152530.340353.3105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 94 )
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 213 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 13 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more