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- EMDB-23306: Cryo-EM structure of human Apo CNGA1 channel in K+/Ca2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-23306
TitleCryo-EM structure of human Apo CNGA1 channel in K+/Ca2+
Map data
Sample
  • Cell: Apo CNGA1 homotetramer in K+/Ca2+
    • Protein or peptide: cGMP-gated cation channel alpha-1
  • Ligand: CHOLESTEROL
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: POTASSIUM IONPotassium
  • Ligand: water
KeywordsALPHA-HELICAL / MEMBRANE PROTEIN / ION CHANNEL
Function / homology
Function and homology information


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / response to stimulus / photoreceptor outer segment membrane / monoatomic cation transmembrane transport / cGMP binding / visual perception / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade ...intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / response to stimulus / photoreceptor outer segment membrane / monoatomic cation transmembrane transport / cGMP binding / visual perception / Activation of the phototransduction cascade / Inactivation, recovery and regulation of the phototransduction cascade / protein-containing complex binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Cyclic nucleotide-gated channel, C-terminal leucine zipper domain / C-terminal leucine zipper domain of cyclic nucleotide-gated channels / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / 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
cGMP-gated cation channel alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsXue J / Han Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Welch Foundation United States
CitationJournal: Neuron / Year: 2021
Title: Structural mechanisms of gating and selectivity of human rod CNGA1 channel.
Authors: Jing Xue / Yan Han / Weizhong Zeng / Yan Wang / Youxing Jiang /
Abstract: Mammalian cyclic nucleotide-gated (CNG) channels play an essential role in the signal transduction of the visual and olfactory sensory systems. Here we reveal the structural mechanism of ligand ...Mammalian cyclic nucleotide-gated (CNG) channels play an essential role in the signal transduction of the visual and olfactory sensory systems. Here we reveal the structural mechanism of ligand gating in human rod CNGA1 channel by determining its cryo-EM structures in both the apo closed and cGMP-bound open states. Distinct from most other members of voltage-gated tetrameric cation channels, CNGA1 forms a central channel gate in the middle of the membrane, occluding the central cavity. Structural analyses of ion binding profiles in the selectivity filters of the wild-type channel and the E365Q filter mutant allow us to unambiguously define the two Ca binding sites inside the selectivity filter, providing structural insights into Ca blockage and permeation in CNG channels. The structure of the E365Q mutant also reveals two alternative side-chain conformations at Q365, providing a plausible explanation for the voltage-dependent gating of CNG channel acquired upon E365 mutation.
History
DepositionJan 18, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lft
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23306.png

Downloads & links

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Map

FileDownload / File: emd_23306.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.844 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07318977 - 0.1380857
Average (Standard dev.)0.00049483456 (±0.0049917754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 243.07199 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8440.8440.844
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z243.072243.072243.072
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ296296296
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0730.1380.000

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Supplemental data

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Sample components

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Entire : Apo CNGA1 homotetramer in K+/Ca2+

EntireName: Apo CNGA1 homotetramer in K+/Ca2+
Components
  • Cell: Apo CNGA1 homotetramer in K+/Ca2+
    • Protein or peptide: cGMP-gated cation channel alpha-1
  • Ligand: CHOLESTEROL
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: POTASSIUM IONPotassium
  • Ligand: water

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Supramolecule #1: Apo CNGA1 homotetramer in K+/Ca2+

SupramoleculeName: Apo CNGA1 homotetramer in K+/Ca2+ / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: cGMP-gated cation channel alpha-1

MacromoleculeName: cGMP-gated cation channel alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.650434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GSASKDKKEE EKKEVVVIDP SGNTYYNWLF CITLPVMYNW TMVIARACFD ELQSDYLEYW LILDYVSDIV YLIDMFVRT RTGYLEQGLL VKEELKLINK YKSNLQFKLD VLSLIPTDLL YFKLGWNYPE IRLNRLLRFS RMFEFFQRTE T RTNYPNIF ...String:
MDYKDDDDKG GSASKDKKEE EKKEVVVIDP SGNTYYNWLF CITLPVMYNW TMVIARACFD ELQSDYLEYW LILDYVSDIV YLIDMFVRT RTGYLEQGLL VKEELKLINK YKSNLQFKLD VLSLIPTDLL YFKLGWNYPE IRLNRLLRFS RMFEFFQRTE T RTNYPNIF RISNLVMYIV IIIHWNACVF YSISKAIGFG NDTWVYPDIN DPEFGRLARK YVYSLYWSTL TLTTIGETPP PV RDSEYVF VVVDFLIGVL IFATIVGNIG SMISNMNAAR AEFQARIDAI KQYMHFRNVS KDMEKRVIKW FDYLWTNKKT VDE KEVLKY LPDKLRAEIA INVHLDTLKK VRIFADCEAG LLVELVLKLQ PQVYSPGDYI CKKGDIGREM YIIKEGKLAV VADD GVTQF VVLSDGSYFG EISILNIKGS KAGNRRTANI KSIGYSDLFC LSKDDLMEAL TEYPDAKTML EEKGKQILMK DGLLD LNIA NAGSDPKDLE EKVTRMEGSV DLLQTRFARI LAEYESMQQK LKQRLTKVEK FLKPLIDTEF SSIEGPGAES GPIDST

UniProtKB: cGMP-gated cation channel alpha-1

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #3: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 24 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 274333
FSC plot (resolution estimation)

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