[English] 日本語
Yorodumi
- EMDB-22201: Cryo-EM structure of the G protein-gated inward rectifier K+ chan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22201
TitleCryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK1/4 (Kir3.1/Kir3.4) in apo form
Map dataCryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK1/4 (Kir3.1/Kir3.4) in apo form
Sample
  • Complex: Hetero-tetrameric assembly of G protein-activated inward rectifier potassium channel 1/4
    • Protein or peptide: G protein-activated inward rectifier potassium channel 1
    • Protein or peptide: G protein-activated inward rectifier potassium channel 4
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / : / G-protein activated inward rectifier potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction ...ventricular cardiac muscle cell membrane repolarization / voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization / : / G-protein activated inward rectifier potassium channel activity / membrane repolarization during atrial cardiac muscle cell action potential / voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of monoatomic ion transmembrane transport / parallel fiber to Purkinje cell synapse / potassium ion import across plasma membrane / regulation of heart rate by cardiac conduction / voltage-gated potassium channel complex / response to electrical stimulus / T-tubule / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / potassium ion transport / external side of plasma membrane / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir3.4 / Potassium channel, inwardly rectifying, Kir3.1 / 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 / Immunoglobulin E-set
Similarity search - Domain/homology
G protein-activated inward rectifier potassium channel 4 / G protein-activated inward rectifier potassium channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsNiu Y / Tao X / MacKinnon R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM43949 United States
CitationJournal: Elife / Year: 2020
Title: Cryo-EM analysis of PIP regulation in mammalian GIRK channels.
Authors: Yiming Niu / Xiao Tao / Kouki K Touhara / Roderick MacKinnon /
Abstract: G-protein-gated inward rectifier potassium (GIRK) channels are regulated by G proteins and PIP. Here, using cryo-EM single particle analysis we describe the equilibrium ensemble of structures of ...G-protein-gated inward rectifier potassium (GIRK) channels are regulated by G proteins and PIP. Here, using cryo-EM single particle analysis we describe the equilibrium ensemble of structures of neuronal GIRK2 as a function of the C8-PIP concentration. We find that PIP shifts the equilibrium between two distinguishable structures of neuronal GIRK (GIRK2), extended and docked, towards the docked form. In the docked form the cytoplasmic domain, to which G binds, becomes accessible to the cytoplasmic membrane surface where G resides. Furthermore, PIP binding reshapes the G binding surface on the cytoplasmic domain, preparing it to receive G. We find that cardiac GIRK (GIRK1/4) can also exist in both extended and docked conformations. These findings lead us to conclude that PIP influences GIRK channels in a structurally similar manner to Kir2.2 channels. In Kir2.2 channels, the PIP-induced conformational changes open the pore. In GIRK channels, they prepare the channel for activation by G.
History
DepositionJun 21, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22201.png

Downloads & links

-
Map

FileDownload / File: emd_22201.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the G protein-gated inward rectifier K+ channel GIRK1/4 (Kir3.1/Kir3.4) in apo form
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.0135 / Movie #1: 0.0135
Minimum - Maximum-0.020268526 - 0.035457663
Average (Standard dev.)0.0000092547 (±0.0019634806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 263.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z263.680263.680263.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0200.0350.000

-
Supplemental data

-
Sample components

-
Entire : Hetero-tetrameric assembly of G protein-activated inward rectifie...

EntireName: Hetero-tetrameric assembly of G protein-activated inward rectifier potassium channel 1/4
Components
  • Complex: Hetero-tetrameric assembly of G protein-activated inward rectifier potassium channel 1/4
    • Protein or peptide: G protein-activated inward rectifier potassium channel 1
    • Protein or peptide: G protein-activated inward rectifier potassium channel 4

-
Supramolecule #1: Hetero-tetrameric assembly of G protein-activated inward rectifie...

SupramoleculeName: Hetero-tetrameric assembly of G protein-activated inward rectifier potassium channel 1/4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: HEK293T

-
Macromolecule #1: G protein-activated inward rectifier potassium channel 1

MacromoleculeName: G protein-activated inward rectifier potassium channel 1
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSALRRKFGD DYQVVTTSSS GSGLQPQGPG QDPQQQLVPK KKRQRFVDKN GRCNVQHGNL GSETSRYLSD LFTTLVDLKW RWNLFIFILT YTVAWLFMAS MWWVIAYTRG DLNKAHVGNY TPCVANVYNF PSAFLFFIET EATIGYGYRY ITDKCPEGII LFLFQSILGS ...String:
MSALRRKFGD DYQVVTTSSS GSGLQPQGPG QDPQQQLVPK KKRQRFVDKN GRCNVQHGNL GSETSRYLSD LFTTLVDLKW RWNLFIFILT YTVAWLFMAS MWWVIAYTRG DLNKAHVGNY TPCVANVYNF PSAFLFFIET EATIGYGYRY ITDKCPEGII LFLFQSILGS IVDAFLIGCM FIKMSQPKKR AETLMFSEHA VISMRDGKLT LMFRVGNLRN SHMVSAQIRC KLLKSRQTPE GEFLPLDQLE LDVGFSTGAD QLFLVSPLTI CHVIDAKSPF YDLSQRSMQT EQFEIVVILE GIVETTGMTC QARTSYTEDE VLWGHRFFPV ISLEEGFFKV DYSQFHATFE VPTPPYSVKE QEEMLLMSSP LIAPAITNSK ERHNSVECLD GLDDITTKLP SKLQKITGRE DFPKKLLRMS STTSEKAYSL GDLPMKLQRI SSVPGNSEEK LVSKTTKMLS DPMSQSVADL PPKLQKMAGG AARMEGNLPA KLRKMNSDRF T

-
Macromolecule #2: G protein-activated inward rectifier potassium channel 4

MacromoleculeName: G protein-activated inward rectifier potassium channel 4
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGDSRNAMN QDMEIGVTPW DPKKIPKQAR DYVPIATDRT RLLAEGKKPR QRYMEKSGKC NVHHGNVQE TYRYLSDLFT TLVDLKWRFN LLVFTMVYTV TWLFFGFIWW LIAYIRGDLD H VGDQEWIP CVENLSGFVS AFLFSIETET TIGYGFRVIT EKCPEGIILL ...String:
MAGDSRNAMN QDMEIGVTPW DPKKIPKQAR DYVPIATDRT RLLAEGKKPR QRYMEKSGKC NVHHGNVQE TYRYLSDLFT TLVDLKWRFN LLVFTMVYTV TWLFFGFIWW LIAYIRGDLD H VGDQEWIP CVENLSGFVS AFLFSIETET TIGYGFRVIT EKCPEGIILL LVQAILGSIV NA FMVGCMF VKISQPKKRA ETLMFSNNAV ISMRDEKLCL MFRVGDLRNS HIVEASIRAK LIK SRQTKE GEFIPLNQTD INVGFDTGDD RLFLVSPLII SHEINQKSPF WEMSQAQLHQ EEFE VVVIL EGMVEATGMT CQARSSYMDT EVLWGHRFTP VLTLEKGFYE VDYNTFHDTY ETNTP SCCA KELAEMKREG RLLQYLPSPP LLGGCAEAGL DAEAEQNEED EPKGLGGSRE ARGSV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Details: 20 mM Tris-HCl pH 7.5, 150 mM KCl, 20 mM DTT, 1 mM DETA, 0.2% DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-50 / Average exposure time: 80.0 sec. / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.0.6)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.0), cryoSPARC (ver. 2.9.0))
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57644

+
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