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- EMDB-63754: CryoEM structure of a transmembrane protein -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63754
TitleCryoEM structure of a transmembrane protein
Map datalocal refinement with transmembrane domain mask
Sample
  • Complex: Heteromeric Kir4.1/5.1 channel in complex with VU0134992 in curly form
    • Protein or peptide: Inward rectifier potassium channel 16
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 10
  • Ligand: POTASSIUM ION
  • Ligand: 2-(2-bromanyl-4-propan-2-yl-phenoxy)-~{N}-(2,2,6,6-tetramethylpiperidin-4-yl)ethanamide
Keywordskir4.1 / kir5.1 / potassium channel / VU0134992 / MEMBRANE 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsNing Y / Ge J / Yu J
Funding support1 items
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, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63754.png

Downloads & links

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Map

FileDownload / File: emd_63754.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement with transmembrane domain mask
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.0579427 - 1.8890907
Average (Standard dev.)0.00019164657 (±0.02341806)
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: local refinement with transmembrane domain mask

Fileemd_63754_additional_1.map
Annotationlocal refinement with transmembrane domain mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: local refinement with transmembrane domain mask

Fileemd_63754_half_map_1.map
Annotationlocal refinement with transmembrane domain mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: local refinement with transmembrane domain mask

Fileemd_63754_half_map_2.map
Annotationlocal refinement with transmembrane domain mask
Projections & Slices
AxesZYX

Projections

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 VU0134992 in curly form

EntireName: Heteromeric Kir4.1/5.1 channel in complex with VU0134992 in curly form
Components
  • Complex: Heteromeric Kir4.1/5.1 channel in complex with VU0134992 in curly form
    • Protein or peptide: Inward rectifier potassium channel 16
    • Protein or peptide: ATP-sensitive inward rectifier potassium channel 10
  • Ligand: POTASSIUM ION
  • Ligand: 2-(2-bromanyl-4-propan-2-yl-phenoxy)-~{N}-(2,2,6,6-tetramethylpiperidin-4-yl)ethanamide

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Supramolecule #1: Heteromeric Kir4.1/5.1 channel in complex with VU0134992 in curly form

SupramoleculeName: Heteromeric Kir4.1/5.1 channel in complex with VU0134992 in curly form
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: 38.99707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYPPEHIIAE KRRARRRLLH KDGSCNVYFK HIFGEWGSYV VDIFTTLVDT KWRHMFVIFS LSYILSWLIF GSVFWLIAFH HGDLLNDPD ITPCVDNVHS FTGAFLFSLE TQTTIGYGYR CVTEECSVAV LMVILQSILS CIINTFIIGA ALAKMATARK R AQTIRFSY ...String:
MYPPEHIIAE KRRARRRLLH KDGSCNVYFK HIFGEWGSYV VDIFTTLVDT KWRHMFVIFS LSYILSWLIF GSVFWLIAFH HGDLLNDPD ITPCVDNVHS FTGAFLFSLE TQTTIGYGYR CVTEECSVAV LMVILQSILS CIINTFIIGA ALAKMATARK R AQTIRFSY FALIGMRDGK LCLMWRIGDF RPNHVVEGTV RAQLLRYTED SEGRMTMAFK DLKLVNDQII LVTPVTIVHE ID HESPLYA LDRKAVAKDN FEILVTFIYT GDSTGTSHQS RSSYVPREIL WGHRFNDVLE VKRKYYKVNC LQFEGSVEVY APF CSAKQL DWKDQQLHIE K

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: 38.984992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIRRRRVLTK DGRSNVRMEH IADKRFLYLK DLWTTFIDMQ WRYKLLLFSA TFAGTWFLFG VVWYLVAVAH GDLLELDPPA NHTPCVVQV HTLTGAFLFS LESQTTIGYG FRYISEECPL AIVLLIAQLV LTTILEIFIT GTFLAKIARP KKRAETIRFS Q HAVVASHN ...String:
MIRRRRVLTK DGRSNVRMEH IADKRFLYLK DLWTTFIDMQ WRYKLLLFSA TFAGTWFLFG VVWYLVAVAH GDLLELDPPA NHTPCVVQV HTLTGAFLFS LESQTTIGYG FRYISEECPL AIVLLIAQLV LTTILEIFIT GTFLAKIARP KKRAETIRFS Q HAVVASHN GKPCLMIRVA NMRKSLLIGC QVTGKLLQTH QTKEGENIRL NQVNVTFQVD TASDSPFLIL PLTFYHVVDE TS PLKDLPL RSGEGDFELV LILSGTVEST SATCQVRTSY LPEEILWGYE FTPAISLSAS GKYIADFSLF DQVVKVASPS GLR DSTVRY GDPEKLKLEE SLREQAEKE

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: 2-(2-bromanyl-4-propan-2-yl-phenoxy)-~{N}-(2,2,6,6-tetramethylpip...

MacromoleculeName: 2-(2-bromanyl-4-propan-2-yl-phenoxy)-~{N}-(2,2,6,6-tetramethylpiperidin-4-yl)ethanamide
type: ligand / ID: 4 / Number of copies: 2 / Formula: A1ENN
Molecular weightTheoretical: 411.376 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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195697
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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