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- PDB-9tg6: Cryo-EM structure of the inward rectifying potassium channel 7.1 ... -

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Basic information

Entry
Database: PDB / ID: 9tg6
TitleCryo-EM structure of the inward rectifying potassium channel 7.1 (Kir7.1) in complex with PIP2
ComponentsInward rectifier potassium channel 13
KeywordsMEMBRANE PROTEIN / potassium ion channel / active conformation / human 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
: / Chem-PIO / Inward rectifier potassium channel 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsO'Malley, N. / Faust, B. / Nasrallah, C. / Wallace, B.A.
Funding support United Kingdom, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inward rectifier potassium channel 13
B: Inward rectifier potassium channel 13
D: Inward rectifier potassium channel 13
C: Inward rectifier potassium channel 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,65212
Polymers169,5094
Non-polymers3,1438
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Inward rectifier potassium channel 13 / Inward rectifier K(+) channel Kir7.1 / Potassium channel / inwardly rectifying subfamily J member 13


Mass: 42377.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNJ13 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O60928
#2: Chemical
ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric assembly of human inward rectifying potassium channel 7.1
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Cellular location: Plasma membrane
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.5
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 31.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 22098

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC3.2particle selectionTemplate Picker
4cryoSPARCv3.2CTF correction
7Coot0.9model fitting
9cryoSPARCv3.2initial Euler assignment
10cryoSPARCv3.2final Euler assignment
11cryoSPARC4.2classification
12cryoSPARC4.23D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8821241
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 556510 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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