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- EMDB-63755: Cryo-EM structure of heteromeric Kir4.1/5.1 potassium channel in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63755
TitleCryo-EM structure of heteromeric Kir4.1/5.1 potassium channel in complex with Ehop-016
Map data
Sample
  • Complex: Heteromeric Kir4.1/5.1 channel in complex with EHop-016
    • Protein or peptide: Inward rectifier potassium channel 16
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 10
  • Ligand: POTASSIUM ION
  • Ligand: ~{N}4-(9-ethylcarbazol-3-yl)-~{N}2-(3-morpholin-4-ylpropyl)pyrimidine-2,4-diamine
Keywordskir4.1 / kir5.1 / membrane protein / EHop-016 / TRANSPORT PROTEIN
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 / non-motile cilium assembly / regulation of monoatomic ion transmembrane transport / 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 / non-motile cilium assembly / regulation of monoatomic ion transmembrane transport / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsNing Y / Ge J / Yu J
Funding support China, 1 items
OrganizationGrant numberCountry
Other government32471016; LG-QS-202203-05; 22PJ1410300 China
CitationJournal: To Be Published
Title: CryoEM structure of a transmembrane protein
Authors: Ning Y / Ge J / Yu J
History
DepositionMar 14, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63755.png

Downloads & links

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Map

FileDownload / File: emd_63755.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.136
Minimum - Maximum-1.66902 - 2.2458456
Average (Standard dev.)0.00042644923 (±0.02778671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63755_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63755_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_63755_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heteromeric Kir4.1/5.1 channel in complex with EHop-016

EntireName: Heteromeric Kir4.1/5.1 channel in complex with EHop-016
Components
  • Complex: Heteromeric Kir4.1/5.1 channel in complex with EHop-016
    • Protein or peptide: Inward rectifier potassium channel 16
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 10
  • Ligand: POTASSIUM ION
  • Ligand: ~{N}4-(9-ethylcarbazol-3-yl)-~{N}2-(3-morpholin-4-ylpropyl)pyrimidine-2,4-diamine

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Supramolecule #1: Heteromeric Kir4.1/5.1 channel in complex with EHop-016

SupramoleculeName: Heteromeric Kir4.1/5.1 channel in complex with EHop-016
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Inward rectifier potassium channel 16

MacromoleculeName: Inward rectifier potassium channel 16 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.861547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ARRRLLHKDG SCNVYFKHIF GEWGSYVVDI FTTLVDTKWR HMFVIFSLSY ILSWLIFGSV FWLIAFHHGD LLNDPDITPC VDNVHSFTG AFLFSLETQT TIGYGYRCVT EECSVAVLMV ILQSILSCII NTFIIGAALA KMATARKRAQ TIRFSYFALI G MRDGKLCL ...String:
ARRRLLHKDG SCNVYFKHIF GEWGSYVVDI FTTLVDTKWR HMFVIFSLSY ILSWLIFGSV FWLIAFHHGD LLNDPDITPC VDNVHSFTG AFLFSLETQT TIGYGYRCVT EECSVAVLMV ILQSILSCII NTFIIGAALA KMATARKRAQ TIRFSYFALI G MRDGKLCL MWRIGDFRPN HVVEGTVRAQ LLRYTEDSEG RMTMAFKDLK LVNDQIILVT PVTIVHEIDH ESPLYALDRK AV AKDNFEI LVTFIYTGDS TGTSHQSRSS YVPREILWGH RFNDVLEVKR KYYKVNCLQF EGSVEVYAPF CSAKQLDWKD QQL

UniProtKB: Inward rectifier potassium channel 16

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Macromolecule #2: ATP-sensitive inward rectifier potassium channel 10

MacromoleculeName: ATP-sensitive inward rectifier potassium channel 10 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.231773 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RRRVLTKDGR SNVRMEHIAD KRFLYLKDLW TTFIDMQWRY KLLLFSATFA GTWFLFGVVW YLVAVAHGDL LELDPPANHT PCVVQVHTL TGAFLFSLES QTTIGYGFRY ISEECPLAIV LLIAQLVLTT ILEIFITGTF LAKIARPKKR AETIRFSQHA V VASHNGKP ...String:
RRRVLTKDGR SNVRMEHIAD KRFLYLKDLW TTFIDMQWRY KLLLFSATFA GTWFLFGVVW YLVAVAHGDL LELDPPANHT PCVVQVHTL TGAFLFSLES QTTIGYGFRY ISEECPLAIV LLIAQLVLTT ILEIFITGTF LAKIARPKKR AETIRFSQHA V VASHNGKP CLMIRVANMR KSLLIGCQVT GKLLQTHQTK EGENIRLNQV NVTFQVDTAS DSPFLILPLT FYHVVDETSP LK DLPLRSG EGDFELVLIL SGTVESTSAT CQVRTSYLPE EILWGYEFTP AISLSASGKY IADFSLFDQV VKVASP

UniProtKB: ATP-sensitive inward rectifier potassium channel 10

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: ~{N}4-(9-ethylcarbazol-3-yl)-~{N}2-(3-morpholin-4-ylpropyl)pyrimi...

MacromoleculeName: ~{N}4-(9-ethylcarbazol-3-yl)-~{N}2-(3-morpholin-4-ylpropyl)pyrimidine-2,4-diamine
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1EM5
Molecular weightTheoretical: 430.545 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 281339
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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