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- EMDB-55889: Cryo-EM structure of the R162W mutant inward rectifying potassium... -

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Basic information

Entry
Database: EMDB / ID: EMD-55889
TitleCryo-EM structure of the R162W mutant inward rectifying potassium channel 7.1 (Kir7.1)
Map data
Sample
  • Complex: Tetrameric assembly of human inward rectifying potassium channel 7.1
    • Protein or peptide: Inward rectifier potassium channel 13
  • Ligand: POTASSIUM ION
Keywordspotassium ion channel / active conformation / human membrane protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / potassium ion import across plasma membrane / monoatomic ion channel complex / potassium ion transport / regulation of membrane potential / plasma membrane
Similarity search - Function
Inward rectifier potassium channel 13 / 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
Inward rectifier potassium channel 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsO'Malley N / Faust B / Nasrallah C / Wallace BA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Commun Biol / Year: 2026
Title: Cryo-EM structure of the human Kir7.1 channel reveals the molecular basis of snowflake vitreoretinal degeneration disease.
Authors: Niamh O'Malley / Chady Nasrallah / Ashton Churchill / Jay Bertrand / Belinda R Faust / B A Wallace /
Abstract: The inward rectifying human potassium channel 7.1 (Kir7.1) is a vital ion channel involved in maintaining cellular homoeostasis and electrical signalling across various tissues and organs, activated ...The inward rectifying human potassium channel 7.1 (Kir7.1) is a vital ion channel involved in maintaining cellular homoeostasis and electrical signalling across various tissues and organs, activated by phosphatidylinositol 4,5-bisphosphate (PIP). A genetically inherited loss-of-function mutation in Kir7.1 (R162W) has been linked to the rare retinal disease Snowflake Vitreoretinal Degeneration (SVD), for which there are currently no curative treatment options. Here, the cryo-EM structures of wild type Kir7.1 and the R162W disease-related variant are presented, which unveil the molecular basis of SVD: the reorientation of the mutant tryptophan side chains into the pore impedes the flow of potassium ions, which would result in the loss of Kir7.1 transport function. Furthermore, this investigation shows that PIP binding widens the helix bundle crossing gate diameter, even in the absence of a docked cytoplasmic domain. This observation contrasts with other Kir-PIP₂ complexes and suggests that Kir7.1 may adopt an intermediate conformation during channel activation. These findings provide a structural basis for Kir7.1 loss of function in SVD and provide a framework for future therapeutic development.
History
DepositionNov 28, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55889.png

Downloads & links

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Map

FileDownload / File: emd_55889.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 440 pix.
= 286. Å		0.65 Å/pix.
x 440 pix.
= 286. Å		0.65 Å/pix.
x 440 pix.
= 286. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-2.0216136 - 2.1077533
Average (Standard dev.)-0.00034398952 (±0.021740207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 286.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55889_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55889_half_map_2.map
Projections & Slices
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Sample components

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Entire : Tetrameric assembly of human inward rectifying potassium channel 7.1

EntireName: Tetrameric assembly of human inward rectifying potassium channel 7.1
Components
  • Complex: Tetrameric assembly of human inward rectifying potassium channel 7.1
    • Protein or peptide: Inward rectifier potassium channel 13
  • Ligand: POTASSIUM ION

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Supramolecule #1: Tetrameric assembly of human inward rectifying potassium channel 7.1

SupramoleculeName: Tetrameric assembly of human inward rectifying potassium channel 7.1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Inward rectifier potassium channel 13

MacromoleculeName: Inward rectifier potassium channel 13 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.534406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKGS MDSSNCKVIA PLLSQRYRRM VTKDGHSTLQ MDGAQRGLAY LRDAWGILMD MRWRWMMLVF SASFVVHWLV FAVLWYVLA EMNGDLELDH DAPPENHTIC VKYITSFTAA FSFSLETQLT IGYGTMFPSG DCPSAIALLA IQMLLGLMLE A FITGAFVA ...String:
DYKDDDDKGS MDSSNCKVIA PLLSQRYRRM VTKDGHSTLQ MDGAQRGLAY LRDAWGILMD MRWRWMMLVF SASFVVHWLV FAVLWYVLA EMNGDLELDH DAPPENHTIC VKYITSFTAA FSFSLETQLT IGYGTMFPSG DCPSAIALLA IQMLLGLMLE A FITGAFVA KIAWPKNRAF SIRFTDTAVV AHMDGKPNLI FQVANTRPSP LTSVRVSAVL YQERENGKLY QTSVDFHLDG IS SDECPFF IFPLTYYHSI TPSSPLATLL QHENPSHFEL VVFLSAMQEG TGEICQRRTS YLPSEIMLHH CFASLLTRGS KGE YQIKME NFDKTVPEFP TPLVSKSPNR TDLDIHINGQ SIDNFQISET GLTEENLYFQ

UniProtKB: Inward rectifier potassium channel 13

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 22098 / Average electron dose: 31.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5871876
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Kir7.1 WT structure previously determined.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140275
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9tg3:
Cryo-EM structure of the R162W mutant inward rectifying potassium channel 7.1 (Kir7.1)

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