[English] 日本語
Yorodumi
- PDB-4nyk: Structure of a membrane protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nyk
TitleStructure of a membrane protein
ComponentsAcid-sensing ion channel 1
KeywordsTRANSPORT PROTEIN / ion channel
Function / homology
Function and homology information


: / Stimuli-sensing channels / ligand-gated sodium channel activity / cellular response to pH / protein homotrimerization / sodium ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
Acid-sensing ion channel domain / acid-sensing ion channel 1 fold / acid-sensing ion channel 1 domain / Acid-sensing ion channels like fold / Acid-sensing ion channels like domains / YojJ-like / Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel ...Acid-sensing ion channel domain / acid-sensing ion channel 1 fold / acid-sensing ion channel 1 domain / Acid-sensing ion channels like fold / Acid-sensing ion channels like domains / YojJ-like / Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acid-sensing ion channel 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBaconguis, I. / Bohlen, C.J. / Goehring, A. / Julius, D. / Gouaux, E.
CitationJournal: Nature / Year: 2009
Title: Pore architecture and ion sites in acid-sensing ion channels and P2X receptors.
Authors: Gonzales, E.B. / Kawate, T. / Gouaux, E.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 12, 2014ID: 3HGC
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acid-sensing ion channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5872
Polymers53,5521
Non-polymers351
Water90150
1
A: Acid-sensing ion channel 1
hetero molecules

A: Acid-sensing ion channel 1
hetero molecules

A: Acid-sensing ion channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,7626
Polymers160,6553
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area16070 Å2
ΔGint-109 kcal/mol
Surface area49050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.787, 131.787, 119.107
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Acid-sensing ion channel 1 / / ASIC1 / Amiloride-sensitive cation channel 2 / neuronal


Mass: 53551.789 Da / Num. of mol.: 1 / Fragment: UNP residues 2-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ASIC1, ACCN2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q1XA76
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: 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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15-0.35 M SODIUM CHLORIDE, 0.1 M HEPES, 23-28% PEG 400, 0.01 M TAURINE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2007
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→80 Å / Num. all: 15481 / Num. obs: 15435 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: dev_1402)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.203 Å / SU ML: 0.42 / σ(F): 1.96 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 793 5.14 %randon
Rwork0.2016 ---
obs0.204 15435 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→41.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 1 50 3276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073309
X-RAY DIFFRACTIONf_angle_d1.0064489
X-RAY DIFFRACTIONf_dihedral_angle_d14.4371185
X-RAY DIFFRACTIONf_chiral_restr0.067491
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.18830.33421360.2642447X-RAY DIFFRACTION100
3.1883-3.43430.27161500.23242439X-RAY DIFFRACTION100
3.4343-3.77970.26871390.1962419X-RAY DIFFRACTION100
3.7797-4.32620.2331320.17772437X-RAY DIFFRACTION100
4.3262-5.44850.20121230.17332461X-RAY DIFFRACTION100
5.4485-41.20670.23771130.21462447X-RAY DIFFRACTION100

+
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