[English] 日本語
Yorodumi
- PDB-3syo: Crystal structure of the G protein-gated inward rectifier K+ chan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3syo
TitleCrystal structure of the G protein-gated inward rectifier K+ channel GIRK2 (Kir3.2) in complex with sodium
ComponentsG protein-activated inward rectifier potassium channel 2
KeywordsMETAL TRANSPORT / ion channel / potassium channel / inward rectification / sodium binding / PIP2 binding / G protein binding
Function / homology
Function and homology information


G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / parallel fiber to Purkinje cell synapse / potassium channel activity / negative regulation of insulin secretion / presynapse ...G-protein activated inward rectifier potassium channel activity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / inward rectifier potassium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / inward rectifier potassium channel activity / parallel fiber to Purkinje cell synapse / potassium channel activity / negative regulation of insulin secretion / presynapse / presynaptic membrane / postsynapse / membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.2 / 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 ...Potassium channel, inwardly rectifying, Kir3.2 / 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
: / G protein-activated inward rectifier potassium channel 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsWhorton, M.R. / MacKinnon, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Crystal Structure of the Mammalian GIRK2 K(+) Channel and Gating Regulation by G Proteins, PIP(2), and Sodium.
Authors: Whorton, M.R. / Mackinnon, R.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: G protein-activated inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3208
Polymers39,0621
Non-polymers2587
Water00
1
A: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
hetero molecules

A: G protein-activated inward rectifier potassium channel 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,27832
Polymers156,2484
Non-polymers1,03028
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area27840 Å2
ΔGint-210 kcal/mol
Surface area49450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.737, 85.737, 178.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-501-

K

21A-502-

K

31A-503-

K

41A-504-

K

51A-505-

K

-
Components

#1: Protein G protein-activated inward rectifier potassium channel 2 / GIRK-2 / Inward rectifier K(+) channel Kir3.2 / Potassium channel / inwardly rectifying subfamily J member 6


Mass: 39061.957 Da / Num. of mol.: 1 / Fragment: UNP residues 52-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Girk2, Kcnj6, Kcnj7, W / Plasmid: pPICZ / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: P48542
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
Has protein modificationY
Sequence detailsUNP P48542 S260T, I313M, AND M344L ARE NATURAL VARIANTS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM sodium citrate, pH 6.0, 1 M sodium chloride, 30-35% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2009
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.54→41.685 Å / Num. obs: 7975 / % possible obs: 92 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.158 / Χ2: 1.605 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.57-3.73.40.7296341.081176.8
3.7-3.854.60.5887311.175186.8
3.85-4.0270.6557671.065191.9
4.02-4.239.50.4618061.125196
4.23-4.59.50.2878281.483196.3
4.5-4.849.70.2178081.606194.9
4.84-5.339.40.188321.626196.6
5.33-6.19.40.1728401.581195.2
6.1-7.6890.128461.925195.1
7.68-41.6857.90.0588832.65190.2

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E4F

2e4f


Resolution: 3.54→41.68 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0.13 / SU B: 55.693 / SU ML: 0.404 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 566 7.1 %RANDOM
Rwork0.2604 ---
obs0.2613 7970 92.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 315.82 Å2 / Biso mean: 140.4722 Å2 / Biso min: 68.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.54→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 7 0 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222446
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9463331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2825306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14423.53599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.23115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.441511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211814
X-RAY DIFFRACTIONr_mcbond_it0.4481.51532
X-RAY DIFFRACTIONr_mcangle_it0.84122465
X-RAY DIFFRACTIONr_scbond_it0.853914
X-RAY DIFFRACTIONr_scangle_it1.5754.5866
LS refinement shellResolution: 3.544→3.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 31 -
Rwork0.301 409 -
all-440 -
obs--71.78 %
Refinement TLS params.Method: refined / Origin x: -9.6666 Å / Origin y: 30.9521 Å / Origin z: -36.7835 Å
111213212223313233
T0.2211 Å20.0025 Å2-0.0836 Å2-0.2329 Å2-0.0823 Å2--0.2223 Å2
L1.5125 °20.3341 °2-0.2975 °2-1.2541 °2-0.9845 °2--2.1424 °2
S-0.0622 Å °0.5383 Å °0.01 Å °-0.404 Å °-0.0029 Å °0.2196 Å °0.2286 Å °-0.1278 Å °0.0651 Å °

+
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