[English] 日本語
Yorodumi
- PDB-3spj: Apo inward rectifier potassium channel Kir2.2 I223L mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3spj
TitleApo inward rectifier potassium channel Kir2.2 I223L mutant
ComponentsInward-rectifier K+ channel Kir2.2
KeywordsMETAL TRANSPORT / PIP / membrane protein / lipid / receptor
Function / homology
Function and homology information


Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization ...Activation of G protein gated Potassium channels / Classical Kir channels / Phase 4 - resting membrane potential / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / monoatomic ion channel complex / potassium ion import across plasma membrane / potassium ion transport / protein homotetramerization / membrane / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.2 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain ...Potassium channel, inwardly rectifying, Kir2.2 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / G protein-activated inward rectifier potassium channel 1 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / Helix Hairpins - #70 / Helix Hairpins / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / ATP-sensitive inward rectifier potassium channel 12 / ATP-sensitive inward rectifier potassium channel 12
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.307 Å
AuthorsHansen, S.B. / Tao, X. / MacKinnon, R.
CitationJournal: Nature / Year: 2011
Title: Structural basis of PIP(2) activation of the classical inward rectifier K(+) channel Kir2.2.
Authors: Hansen, S.B. / Tao, X. / Mackinnon, R.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inward-rectifier K+ channel Kir2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5576
Polymers39,3621
Non-polymers1955
Water0
1
A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules

A: Inward-rectifier K+ channel Kir2.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,22924
Polymers157,4474
Non-polymers78220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area22460 Å2
ΔGint-112 kcal/mol
Surface area57800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.769, 83.769, 197.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-501-

K

21A-502-

K

31A-503-

K

41A-504-

K

51A-505-

K

-
Components

#1: Protein Inward-rectifier K+ channel Kir2.2 / inward rectifier potassium channel 2.2


Mass: 39361.723 Da / Num. of mol.: 1 / Mutation: I223L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: Kir2.2 / Production host: Pichia pastoris (fungus) / References: UniProt: D2YW45, UniProt: F1NHE9*PLUS
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10.62% PEG400, 0.5 M sodium chloride, 0.05 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 10028 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.0118 / Net I/σ(I): 14.5
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.0526 / Mean I/σ(I) obs: 3.7 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7_650)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SPH
Resolution: 3.307→28.364 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 28.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 465 4.8 %
Rwork0.2351 --
obs0.2365 9689 95.58 %
all-10028 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.946 Å2 / ksol: 0.291 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5338 Å2-0 Å20 Å2
2---4.5338 Å2-0 Å2
3---9.0677 Å2
Refinement stepCycle: LAST / Resolution: 3.307→28.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 5 0 2549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082636
X-RAY DIFFRACTIONf_angle_d0.8773521
X-RAY DIFFRACTIONf_dihedral_angle_d15.717939
X-RAY DIFFRACTIONf_chiral_restr0.06401
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3071-3.78470.31881390.27422951X-RAY DIFFRACTION92
3.7847-4.76460.2481760.19163129X-RAY DIFFRACTION98
4.7646-28.3650.26611500.24763144X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.356-0.60291.16024.33912.51921.98140.45040.22650.6370.30730.03420.4046-1.1527-0.9040.00031.01770.16280.20881.1536-0.02541.316-10.68397.8013-36.7186
24.8185-0.04990.65524.4971-0.04062.1520.0930.2234-0.5478-0.4461-0.07860.33080.6454-0.285501.2986-0.169-0.05051.2016-0.11960.9896-12.538-17.048321.6646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 70:188))
2X-RAY DIFFRACTION2chain 'A' and ((resseq 43:60) or (resseq 189:372))

+
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