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- EMDB-30334: Cryo-EM Structure of the Hyperpolarization-Activated Inwardly Rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-30334
TitleCryo-EM Structure of the Hyperpolarization-Activated Inwardly Rectifying Potassium Channel KAT1 from Arabidopsis
Map data
Sample
  • Complex: KAT1
    • Protein or peptide: Potassium channel KAT1
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsHyperpolarization-Activated Inwardly Rectifying Potassium Channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / identical protein binding / plasma membrane
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Potassium channel KAT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi SY / Yang F
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31600601 China
National Natural Science Foundation of China (NSFC)21778051 China
National Natural Science Foundation of China (NSFC)21825703 China
CitationJournal: Cell Res / Year: 2020
Title: Cryo-EM structure of the hyperpolarization-activated inwardly rectifying potassium channel KAT1 from Arabidopsis.
Authors: Siyu Li / Fan Yang / Demeng Sun / Yong Zhang / Mengge Zhang / Sanling Liu / Peng Zhou / Chaowei Shi / Longhua Zhang / Changlin Tian /
History
DepositionJun 9, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cal
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7cal
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30334.png

Downloads & links

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Map

FileDownload / File: emd_30334.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.02
Minimum - Maximum-0.06807749 - 0.124252856
Average (Standard dev.)0.0001983448 (±0.0037154148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0680.1240.000

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Supplemental data

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Sample components

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Entire : KAT1

EntireName: KAT1
Components
  • Complex: KAT1
    • Protein or peptide: Potassium channel KAT1
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: KAT1

SupramoleculeName: KAT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Potassium channel KAT1

MacromoleculeName: Potassium channel KAT1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.361445 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSISWTRNFF ERFCVEEYNI DTIKQSSFLS ADLLPSLGAR INQSTKLRKH IISPFNPRYR AWEMWLVLLV IYSAWICPFQ FAFITYKKD AIFIIDNIVN GFFAIDIILT FFVAYLDSHS YLLVDSPKKI AIRYLSTWFA FDVCSTAPFQ PLSLLFNYNG S ELGFRILS ...String:
MSISWTRNFF ERFCVEEYNI DTIKQSSFLS ADLLPSLGAR INQSTKLRKH IISPFNPRYR AWEMWLVLLV IYSAWICPFQ FAFITYKKD AIFIIDNIVN GFFAIDIILT FFVAYLDSHS YLLVDSPKKI AIRYLSTWFA FDVCSTAPFQ PLSLLFNYNG S ELGFRILS MLRLWRLRRV SSLFARLEKD IRFNYFWIRC TKLISVTLFA IHCAGCFNYL IADRYPNPRK TWIGAVYPNF KE ASLWNRY VTALYWSITT LTTTGYGDFH AENPREMLFD IFFMMFNLGL TAYLIGNMTN LVVHWTSRTR TFRDSVRAAS EFA SRNQLP HDIQDQMLSH ICLKFKTEGL KQQETLNNLP KAIRSSIANY LFFPIVHNIY LFQGVSRNFL FQLVSDIDAE YFPP KEDII LQNEAPTDLY ILVSGAVDFT VYVDGHDQFQ GKAVIGETFG EVGVLYYRPQ PFTVRTTELS QILRISRTSL MSAMH AHAD DGRVIMNNLF MKLRGQQSIA IDDSNTSGHE NRDFKSMGWE EWRDSRKDGY GLDVTNPTSD TALMDAIHKE DTEMVK KIL KEQKIERAKV ERSSSETAGR SYANDSSKKD PYCSSSNQII KPCKREEKRV TIHMMSESKN GKLILLPSSI EELLRLA SE KFGGCNFTKI TNADNAEIDD LDVIWDGDHL YFSSN

UniProtKB: Potassium channel KAT1

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Macromolecule #2: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 2 / Number of copies: 4 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION
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: RANDOM CONICAL TILT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111658
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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