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

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Basic information

Entry
Database: PDB / ID: 9tfv
TitleCryo-EM structure of the inward rectifying potassium channel 7.1 (Kir7.1)
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
: / Inward rectifier potassium channel 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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: To Be Published
Title: Cryo-EM structure of human Kir7.1 reveals the molecular basis of Snowflake Vitreoretinal Degeneration
Authors: O'Malley, N. / Nasrallah, C. / Churchill, A. / Bertrand, J. / Faust, B. / Wallace, B.A.
History
DepositionNov 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
C: Inward rectifier potassium channel 13
D: Inward rectifier potassium channel 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,9206
Polymers166,8424
Non-polymers782
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: 41710.543 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): Expi293F / Production host: Homo sapiens (human) / Strain (production host): HEK293 / References: UniProt: O60928
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
Has ligand of interestN
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)
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 real images: 22098

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.2particle selection
9PHENIX1.21_5207model refinement
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5871876
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 382328 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 34.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338952
ELECTRON MICROSCOPYf_angle_d0.505912220
ELECTRON MICROSCOPYf_chiral_restr0.04221440
ELECTRON MICROSCOPYf_plane_restr0.00381540
ELECTRON MICROSCOPYf_dihedral_angle_d3.96961216

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