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- PDB-9mag: CryoEM structure of a transmembrane protein -

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Basic information

Entry
Database: PDB / ID: 9mag
TitleCryoEM structure of a transmembrane protein
Components
  • ATP-sensitive inward rectifier potassium channel 10
  • Inward rectifier potassium channel 16
KeywordsMEMBRANE PROTEIN / kir4.1 / kir5.1 / VU0134992
Function / homology
Function and homology information


Potassium transport channels / glutamate reuptake / ATP-activated inward rectifier potassium channel activity / central nervous system myelination / regulation of resting membrane potential / potassium ion homeostasis / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / non-motile cilium assembly / cellular response to potassium ion ...Potassium transport channels / glutamate reuptake / ATP-activated inward rectifier potassium channel activity / central nervous system myelination / regulation of resting membrane potential / potassium ion homeostasis / inward rectifier potassium channel activity / regulation of monoatomic ion transmembrane transport / non-motile cilium assembly / cellular response to potassium ion / adult walking behavior / astrocyte projection / ciliary base / potassium ion import across plasma membrane / monoatomic ion channel complex / voltage-gated potassium channel complex / visual perception / potassium ion transmembrane transport / potassium ion transport / regulation of long-term neuronal synaptic plasticity / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / presynapse / cell body / basolateral plasma membrane / ATP binding / plasma membrane
Similarity search - Function
Potassium channel, inwardly rectifying, Kir5 / Potassium channel, inwardly rectifying, Kir1.2 / 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
: / : / ATP-sensitive inward rectifier potassium channel 10 / Inward rectifier potassium channel 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsNing, Y. / Ge, J. / Yu, J.
Funding support1items
OrganizationGrant numberCountry
Other governmentLG-QS-202203-05; 22PJ1410300; 32471016
CitationJournal: To Be Published
Title: CryoEM structure of a transmembrane protein
Authors: Ning, Y. / Ge, J. / Yu, J.
History
DepositionMar 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 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 16
D: ATP-sensitive inward rectifier potassium channel 10
C: Inward rectifier potassium channel 16
B: ATP-sensitive inward rectifier potassium channel 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,9049
Polymers155,9644
Non-polymers9405
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Inward rectifier potassium channel 16 / Inward rectifier K(+) channel Kir5.1 / Potassium channel / inwardly rectifying subfamily J member 16


Mass: 38997.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNJ16 / Production host: Homo sapiens (human) / References: UniProt: Q9NPI9
#2: Protein ATP-sensitive inward rectifier potassium channel 10 / ATP-dependent inwardly rectifying potassium channel Kir4.1 / Inward rectifier K(+) channel Kir1.2 / ...ATP-dependent inwardly rectifying potassium channel Kir4.1 / Inward rectifier K(+) channel Kir1.2 / Potassium channel / inwardly rectifying subfamily J member 10


Mass: 38984.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNJ10 / Production host: Homo sapiens (human) / References: UniProt: P78508
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1ENN / 2-(2-bromanyl-4-propan-2-yl-phenoxy)-~{N}-(2,2,6,6-tetramethylpiperidin-4-yl)ethanamide


Mass: 411.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
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: Heteromeric Kir4.1/5.1 channel in complex with VU0134992 in straight form
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200895 / Symmetry type: POINT
RefinementHighest resolution: 3.37 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210458
ELECTRON MICROSCOPYf_angle_d0.52314208
ELECTRON MICROSCOPYf_dihedral_angle_d4.0731390
ELECTRON MICROSCOPYf_chiral_restr0.0411630
ELECTRON MICROSCOPYf_plane_restr0.0041762

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