[English] 日本語
Yorodumi
- PDB-4d01: Crystal Structure of the Extracellular Domain of the Human Alpha9... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d01
TitleCrystal Structure of the Extracellular Domain of the Human Alpha9 Nicotinic Acetylcholine Receptor
ComponentsNEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
KeywordsSIGNALING PROTEIN / LIGAND BINDING DOMAIN / CYS-LOOP RECEPTOR
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / detection of mechanical stimulus involved in sensory perception of sound / response to auditory stimulus / acetylcholine-gated monoatomic cation-selective channel activity / inner ear morphogenesis / membrane depolarization / transmembrane transporter complex / calcium channel activity ...Acetylcholine inhibits contraction of outer hair cells / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / detection of mechanical stimulus involved in sensory perception of sound / response to auditory stimulus / acetylcholine-gated monoatomic cation-selective channel activity / inner ear morphogenesis / membrane depolarization / transmembrane transporter complex / calcium channel activity / transmembrane signaling receptor activity / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / neuron projection / synapse / plasma membrane
Similarity search - Function
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 ...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
Neuronal acetylcholine receptor subunit alpha-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.795 Å
AuthorsGiastas, P. / Zouridakis, M. / Zarkadas, E. / Tzartos, S.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Crystal Structures of Free and Antagonist-Bound States of Human Alpha9 Nicotinic Receptor Extracellular Domain
Authors: Zouridakis, M. / Giastas, P. / Zarkadas, E. / Chroni-Tzartou, D. / Bregestovski, P. / Tzartos, S.J.
History
DepositionApr 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Nov 19, 2014Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9987
Polymers25,3071
Non-polymers6916
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.520, 64.269, 80.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2072-

HOH

-
Components

#1: Protein NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NICOTINIC ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NACHR ALPHA-9 / HUMAN ALPHA9 NICOTINIC ...NICOTINIC ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NACHR ALPHA-9 / HUMAN ALPHA9 NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 25307.029 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: Q9UGM1
#2: 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


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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRACELLULAR DOMAIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM SPG BUFFER PH 6.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→42 Å / Num. obs: 24313 / % possible obs: 99.3 % / Observed criterion σ(I): 1.4 / Redundancy: 12.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.9
Reflection shellResolution: 1.79→42 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.2 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QC1

2qc1


Resolution: 1.795→42.126 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 28.07 / Stereochemistry target values: ML
Details: RESIDUES OF THE REGION 100-104 WAS EITHER LEFT UNMODELED OR WAS MODELED ONLY THEIR MAIN CHAIN ATOMS
RfactorNum. reflection% reflection
Rfree0.2497 1240 5.1 %
Rwork0.195 --
obs0.196 24313 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 1.795→42.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 44 206 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131840
X-RAY DIFFRACTIONf_angle_d1.4592509
X-RAY DIFFRACTIONf_dihedral_angle_d13.344664
X-RAY DIFFRACTIONf_chiral_restr0.082274
X-RAY DIFFRACTIONf_plane_restr0.008323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7945-1.86640.40051230.33092380X-RAY DIFFRACTION93
1.8664-1.95130.31331610.26172517X-RAY DIFFRACTION99
1.9513-2.05420.29041400.24292551X-RAY DIFFRACTION100
2.0542-2.18290.23851430.2112533X-RAY DIFFRACTION99
2.1829-2.35140.28861370.21842554X-RAY DIFFRACTION100
2.3514-2.5880.26071350.20672570X-RAY DIFFRACTION99
2.588-2.96240.26941210.19532581X-RAY DIFFRACTION99
2.9624-3.7320.24241480.1722605X-RAY DIFFRACTION100
3.732-42.13770.21581320.16452782X-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)
12.08510.7469-1.3763.161-1.64663.4929-0.37990.1475-0.2122-0.5524-0.1809-0.90780.21880.65310.57110.4652-0.10770.12610.39360.02660.491448.761335.985412.5707
21.32980.0962-0.45081.71670.08271.6332-0.27650.30350.159-0.2470.0821-0.0276-0.231-0.24870.15620.377-0.0076-0.0620.31050.00920.274533.777542.380519.4146
37.13082.9227-0.87222.6267-0.62560.577-0.01960.42340.1323-0.1227-0.09670.2384-0.3878-0.3287-0.00030.40810.0166-0.00780.4347-0.10890.38732.229539.599618.0307
42.2865-0.0691-0.30391.3472-0.32361.4802-0.05010.16510.26470.0106-0.05110.1903-0.2033-0.32440.09090.32290.048-0.0460.2854-0.04850.265322.501242.382931.533
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 116 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 117 THROUGH 215 )

+
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://pdbjlvh1.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