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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
Keywordsion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / response to odorant / intracellular cyclic nucleotide activated cation channel complex / protein localization to organelle / intracellularly cGMP-activated cation channel activity / : / detection of light stimulus involved in visual perception ...olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / response to odorant / intracellular cyclic nucleotide activated cation channel complex / protein localization to organelle / intracellularly cGMP-activated cation channel activity / : / detection of light stimulus involved in visual perception / VxPx cargo-targeting to cilium / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment / Golgi-associated vesicle membrane / photoreceptor cell maintenance / retina homeostasis / ciliary membrane / photoreceptor outer segment membrane / sodium ion transport / sodium channel activity / monoatomic cation transmembrane transport / transmembrane transporter complex / monoatomic cation transport / cGMP binding / membrane depolarization / ligand-gated monoatomic ion channel activity / photoreceptor outer segment / phototransduction / regulation of cytosolic calcium ion concentration / cAMP binding / visual perception / potassium ion transport / terminal bouton / calcium channel activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / calcium ion transport / sensory perception of smell / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of gene expression / 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-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
Cyclic nucleotide-gated channel alpha-1 / Cyclic nucleotide-gated channel beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsXue J / Han 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-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 288 pix.
= 242.496 Å		0.84 Å/pix.
x 288 pix.
= 242.496 Å		0.84 Å/pix.
x 288 pix.
= 242.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.842 Å
Density

Histogram

Histogram (log scale)
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)

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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

UniProtKB: Cyclic nucleotide-gated channel alpha-1

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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

UniProtKB: Cyclic nucleotide-gated channel beta-1

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

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Image processing

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

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