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- EMDB-12718: The structure of the native CNGA1/CNGB1 CNG channel from retinal rods -

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Basic information

Entry
Database: EMDB / ID: EMD-12718
TitleThe structure of the native CNGA1/CNGB1 CNG channel from retinal rods
Map data
Sample
  • Complex: Native CNGA1/CNGB1a channel
    • 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


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / transmembrane transporter complex / response to stimulus / photoreceptor outer segment membrane / monoatomic cation transmembrane transport / monoatomic cation transport ...intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / transmembrane transporter complex / response to stimulus / photoreceptor outer segment membrane / monoatomic cation transmembrane transport / monoatomic cation transport / cGMP binding / photoreceptor outer segment / cAMP binding / visual perception / sensory perception of smell / membrane => GO:0016020 / protein-containing complex binding / positive regulation of gene expression / protein homodimerization activity / protein-containing complex / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cyclic nucleotide-gated cation channel beta-1 / 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 cation channel beta-1 / 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 speciesBos taurus (cattle) / Bovine (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBarret DCA / Marino J
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation19082 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: The structure of the native CNGA1/CNGB1 CNG channel from bovine retinal rods.
Authors: Diane C A Barret / Gebhard F X Schertler / U Benjamin Kaupp / Jacopo Marino /
Abstract: In rod photoreceptors of the retina, the cyclic nucleotide-gated (CNG) channel is composed of three CNGA and one CNGB subunits, and it closes in response to light activation to generate an electrical ...In rod photoreceptors of the retina, the cyclic nucleotide-gated (CNG) channel is composed of three CNGA and one CNGB subunits, and it closes in response to light activation to generate an electrical signal that is conveyed to the brain. Here we report the cryo-EM structure of the closed state of the native rod CNG channel isolated from bovine retina. The structure reveals differences between CNGA1 and CNGB1 subunits. Three CNGA1 subunits are tethered at their C terminus by a coiled-coil region. The C-helix in the cyclic nucleotide-binding domain of CNGB1 features a different orientation from that in the three CNGA1 subunits. The arginine residue R994 of CNGB1 reaches into the ionic pathway and blocks the pore, thus introducing an additional gate, which is different from the central hydrophobic gate known from homomeric CNGA channels. These results address the long-standing question of how CNGB1 subunits contribute to the function of CNG channels in visual and olfactory neurons.
History
DepositionApr 6, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o4h
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12718.png

Downloads & links

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Map

FileDownload / File: emd_12718.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.051 / Movie #1: 0.045
Minimum - Maximum-0.121877626 - 0.24248856
Average (Standard dev.)-8.139876e-05 (±0.0064018196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1220.242-0.000

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Supplemental data

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Sample components

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Entire : Native CNGA1/CNGB1a channel

EntireName: Native CNGA1/CNGB1a channel
Components
  • Complex: Native CNGA1/CNGB1a channel
    • 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: Native CNGA1/CNGB1a channel

SupramoleculeName: Native CNGA1/CNGB1a channel / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: purified from rod outer segments
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 356 KDa

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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: Bovine (cattle)
Molecular weightTheoretical: 79.712164 KDa
SequenceString: MKKVIINTWH SFVNIPNVVG PDVEKEITRM ENGACSSFSG DDDDSASMFE ESETENPHAR DSFRSNTHGS GQPSQREQYL PGAIALFNV NNSSNKEQEP KEKKKKKKEK KSKPDDKNEN KKDPEKKKKK EKDKDKKKKE EKGKDKKEEE KKEVVVIDPS G NTYYNWLF ...String:
MKKVIINTWH SFVNIPNVVG PDVEKEITRM ENGACSSFSG DDDDSASMFE ESETENPHAR DSFRSNTHGS GQPSQREQYL PGAIALFNV NNSSNKEQEP KEKKKKKKEK KSKPDDKNEN KKDPEKKKKK EKDKDKKKKE EKGKDKKEEE KKEVVVIDPS G NTYYNWLF CITLPVMYNW TMIIARACFD ELQSDYLEYW LAFDYLSDVV YLLDMFVRTR TGYLEQGLLV KEERKLIDKY KS TFQFKLD VLSVIPTDLL YIKFGWNYPE IRLNRLLRIS RMFEFFQRTE TRTNYPNIFR ISNLVMYIII IIHWNACVYF SIS KAIGFG NDTWVYPDVN DPDFGRLARK YVYSLYWSTL TLTTIGETPP PVRDSEYFFV VADFLIGVLI FATIVGNIGS MISN MNAAR AEFQARIDAI KQYMHFRNVS KDMEKRVIKW FDYLWTNKKT VDEREVLKYL PDKLRAEIAI NVHLDTLKKV RIFAD CEAG LLVELVLKLQ PQVYSPGDYI CKKGDIGREM YIIKEGKLAV VADDGITQFV VLSDGSYFGE ISILNIKGSK AGNRRT ANI KSIGYSDLFC LSKDDLMEAL TEYPDAKGML EEKGKQILMK DGLLDINIAN AGSDPKDLEE KVTRMESSVD LLQTRFA RI LAEYESMQQK LKQRLTKVEK FLKPLIDTEF SAIEGSGTES GPTDSTQD

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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: Bovine (cattle)
Molecular weightTheoretical: 155.228562 KDa
SequenceString: MLGWVQRVLP QPPGTPQKTK QEEEGTEPEP ELEPKPETAP EETELEEVSL PPEEPCVGKE VAAVTLGPQG TQETALTPPT SLQAQVSVA PEAHSSPRGW VLTWLRKGVE KVVPQPAHSS RPSQNIAAGL ESPDQQAGAQ ILGQCGTGGS DEPSEPSRAE D PGPGPWLL ...String:
MLGWVQRVLP QPPGTPQKTK QEEEGTEPEP ELEPKPETAP EETELEEVSL PPEEPCVGKE VAAVTLGPQG TQETALTPPT SLQAQVSVA PEAHSSPRGW VLTWLRKGVE KVVPQPAHSS RPSQNIAAGL ESPDQQAGAQ ILGQCGTGGS DEPSEPSRAE D PGPGPWLL RWFEQNLEKM LPQPPKISEG WRDEPTDAAL GPEPPGPALE IKPMLQAQES PSLPAPGPPE PEEEPIPEPQ PT IQASSLP PPQDSARLMA WILHRLEMAL PQPVIRGKGG EQESDAPVTC DVQTISILPG EQEESHLILE EVDPHWEEDE HQE GSTSTS PRTSEAAPAD EEKGKVVEQT PRELPRIQEE KEDEEEEKED GEEEEEEGRE KEEEEGEEKE EEEGREKEEE EGEK KEEEG REKEEEEGGE KEDEEGREKE EEEGRGKEEE EGGEKEEEEG RGKEEVEGRE EEEDEEEEQD HSVLLDSYLV PQSEE DRSE ESETQDQSEV GGAQAQGEVG GAQALSEESE TQDQSEVGGA QDQSEVGGAQ AQGEVGGAQE QDGVGGAQDQ STSHQE LQE EALADSSGVP ATEEHPELQV EDADADSRPL IAEENPPSPV QLPLSPAKSD TLAVPGSATG SLRKRLPSQD DEAEELK ML SPAASPVVAW SDPTSPQGTD DQDRATSTAS QNSAIINDRL QELVKLFKER TEKVKEKLID PDVTSDEESP KPSPAKKA P EPAPEVKPAE AGQVEEEHYC EMLCCKFKRR PWKKYQFPQS IDPLTNLMYI LWLFFVVLAW NWNCWLIPVR WAFPYQTPD NIHLWLLMDY LCDLIYLLDI TVFQMRLQFV RGGDIITDKK EMRNNYVKSQ RFKMDMLCLL PLDLLYLKFG VNPLLRLPRC LKYMAFFEF NNRLESILSK AYVYRVIRTT AYLLYSLHLN SCLYYWASAY EGLGSTHWVY DGVGNSYIRC YYWAVKTLIT I GGLPDPRT LFEIVFQGLN YFTGVFAFSV MIGQMRDVVG AATAGQTYYR SCMDSTVKYM NFYKIPRSVQ NRVKTWYEYT WH SQGMLDE SELMVQLPDK MRLDLAIDVN YSIVSKVALF QGCDRQMIFD MLKRLRSVVY LPNDYVCKKG EIGREMYIIQ AGQ VQVLGG PDGKSVLVTL KAGSVFGEIS LLAVGGGNRR TANVVAHGFT NLFILDKKDL NEILVHYPES QKLLRKKARR MLRN NNKPK EKSVLILPPR AGTPKLFNAA LAAAGKMGAK GGRGGRLALL RARLKELAAL EAAARQQQLL EQAKSSEDAA VGEEG SASP EQPPRPEPPA PEAPAPEPTA PEPLAPEAPA PEAPAPSSPP PASQERPEGD KDAARPEEHP VRIHVTLGPD PSEQIL LVE VPEKQEEKEK KEEETEEKEE GEEARKEKEE E

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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

Concentration0.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118084

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