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- EMDB-24458: Cryo-EM structure of human rod CNGA1/B1 channel in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-24458
TitleCryo-EM structure of human rod CNGA1/B1 channel in apo state
Map data
Sample
  • Complex: human rod Apo CNGA1/B1 channel in closed state
    • Protein or peptide: cGMP-gated cation channel alpha-1
    • Protein or peptide: Cyclic nucleotide-gated cation channel beta-1
Function / homology
Function and homology information


olfactory nerve maturation / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / detection of light stimulus involved in visual perception / response to odorant / protein localization to organelle / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / intracellularly cAMP-activated cation channel activity ...olfactory nerve maturation / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / detection of light stimulus involved in visual perception / response to odorant / protein localization to organelle / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / intracellularly cAMP-activated cation channel activity / VxPx cargo-targeting to cilium / Golgi-associated vesicle membrane / transmembrane transporter complex / photoreceptor cell maintenance / retina homeostasis / response to stimulus / ciliary membrane / photoreceptor outer segment membrane / monoatomic cation transmembrane transport / membrane depolarization / ligand-gated monoatomic ion channel activity / monoatomic cation transport / phototransduction / cGMP binding / photoreceptor outer segment / cAMP binding / regulation of cytosolic calcium ion concentration / visual perception / Olfactory Signaling Pathway / Activation of the phototransduction cascade / terminal bouton / Inactivation, recovery and regulation of the phototransduction cascade / protein-containing complex binding / positive regulation of gene expression / 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 / Cyclic nucleotide-gated cation channel beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsXue J / Han Y / Jiang Y
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140892 United States
Welch FoundationI-1578 United States
Howard Hughes Medical Institute (HHMI) 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
DepositionJul 16, 2021-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rh9
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24458.png

Downloads & links

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Map

FileDownload / File: emd_24458.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.842 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.07331263 - 0.15152933
Average (Standard dev.)0.00040030826 (±0.0061939694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 242.496 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8420.8420.842
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z242.496242.496242.496
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0730.1520.000

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Supplemental data

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Sample components

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Entire : human rod Apo CNGA1/B1 channel in closed state

EntireName: human rod Apo CNGA1/B1 channel in closed state
Components
  • Complex: human rod Apo CNGA1/B1 channel in closed state
    • Protein or peptide: cGMP-gated cation channel alpha-1
    • Protein or peptide: Cyclic nucleotide-gated cation channel beta-1

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Supramolecule #1: human rod Apo CNGA1/B1 channel in closed state

SupramoleculeName: human rod Apo CNGA1/B1 channel in closed state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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: 3 / 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

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Macromolecule #2: Cyclic nucleotide-gated cation channel beta-1

MacromoleculeName: Cyclic nucleotide-gated cation channel beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.039305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GSASSGVPAT KQHPEVQVED TDADSCPLMA EENPPSTVLP PPSPAKSDTL IVPSSASGTH RKKLPSEDDE AEELKALSP AESPVVAWSD PTTPKDTDGQ DRAASTASTN SAIINDRLQE LVKLFKERTE KVKEKLIDPD VTSDEESPKP S PAKKAPEP ...String:
MDYKDDDDKG GSASSGVPAT KQHPEVQVED TDADSCPLMA EENPPSTVLP PPSPAKSDTL IVPSSASGTH RKKLPSEDDE AEELKALSP AESPVVAWSD PTTPKDTDGQ DRAASTASTN SAIINDRLQE LVKLFKERTE KVKEKLIDPD VTSDEESPKP S PAKKAPEP APDTKPAEAE PVEEEHYCDM LCCKFKHRPW KKYQFPQSID PLTNLMYVLW LFFVVMAWNW NCWLIPVRWA FP YQTPDNI HHWLLMDYLC DLIYFLDITV FQTRLQFVRG GDIITDKKDM RNNYLKSRRF KMDLLSLLPL DFLYLKVGVN PLL RLPRCL KYMAFFEFNS RLESILSKAY VYRVIRTTAY LLYSLHLNSC LYYWASAYQG LGSTHWVYDG VGNSYIRCYY FAVK TLITI GGLPDPKTLF EIVFQLLNYF TGVFAFSVMI GQMRDVVGAA TAGQTYYRSC MDSTVKYMNF YKIPKSVQNR VKTWY EYTW HSQGMLDESE LMVQLPDKMR LDLAIDVNYN IVSKVALFQG CDRQMIFDML KRLRSVVYLP NDYVCKKGEI GREMYI IQA GQVQVLGGPD GKSVLVTLKA GSVFGEISLL AVGGGNRRTA NVVAHGFTNL FILDKKDLNE ILVHYPESQK LLRKKAR RM LRSNNKPKEE KSVLILPPRA GTPKLFNAAL AMTGKMGGKG AKGGKLAHLR ARLKELAALE AAAKQQELVE QAKSSQDV K GEEGSAAPDQ HTHPKEAATD PPAPRTPPEP PGSPPSSPPP ASLGRPEGEE EGPAEPEEHS VRICMSPGPE PGEQILSVK MPEEREEKAE

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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

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 687702

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