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- PDB-7o4h: The structure of the native CNGA1/CNGB1 CNG channel from retinal rods -

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Basic information

Entry
Database: PDB / ID: 7o4h
TitleThe structure of the native CNGA1/CNGB1 CNG channel from retinal rods
Components
  • Cyclic nucleotide-gated cation channel beta-1
  • cGMP-gated cation channel alpha-1
KeywordsMEMBRANE PROTEIN / CNG channel / CNGA1 / CNGB1 / rod
Function / homology
Function and homology information


intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / Inactivation, recovery and regulation of the phototransduction cascade / intracellularly cAMP-activated cation channel activity / Activation of the phototransduction cascade / molecular sequestering activity / response to stimulus / retina homeostasis / photoreceptor outer segment membrane / sodium ion transport ...intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / Inactivation, recovery and regulation of the phototransduction cascade / intracellularly cAMP-activated cation channel activity / Activation of the phototransduction cascade / molecular sequestering activity / response to stimulus / retina homeostasis / photoreceptor outer segment membrane / sodium ion transport / monoatomic cation transmembrane transport / monoatomic cation transport / photoreceptor outer segment / cGMP binding / transmembrane transporter complex / cAMP binding / visual perception / calcium ion transport / sensory perception of smell / molecular adaptor activity / positive regulation of gene expression / protein-containing complex binding / protein homodimerization activity / protein-containing complex / identical protein binding / plasma membrane / cytoplasm
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
Cyclic nucleotide-gated channel alpha-1 / Cyclic nucleotide-gated channel beta-1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBarret, D.C.A. / Marino, J.
Funding support Switzerland, 1items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: cGMP-gated cation channel alpha-1
B: cGMP-gated cation channel alpha-1
C: cGMP-gated cation channel alpha-1
D: Cyclic nucleotide-gated cation channel beta-1


Theoretical massNumber of molelcules
Total (without water)394,3654
Polymers394,3654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15700 Å2
ΔGint-145 kcal/mol
Surface area111670 Å2
MethodPISA

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Components

#1: Protein cGMP-gated cation channel alpha-1 / Cyclic nucleotide-gated cation channel 1 / Cyclic nucleotide-gated channel alpha-1 / CNG channel ...Cyclic nucleotide-gated cation channel 1 / Cyclic nucleotide-gated channel alpha-1 / CNG channel alpha-1 / CNG-1 / CNG1 / Cyclic nucleotide-gated channel / photoreceptor / Rod photoreceptor cGMP-gated channel subunit alpha


Mass: 79712.164 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q00194
#2: Protein Cyclic nucleotide-gated cation channel beta-1 / 240 kDa protein of rod photoreceptor CNG-channel / Cyclic nucleotide-gated cation channel 4 / CNG ...240 kDa protein of rod photoreceptor CNG-channel / Cyclic nucleotide-gated cation channel 4 / CNG channel 4 / CNG-4 / CNG4 / Cyclic nucleotide-gated cation channel gamma / Cyclic nucleotide-gated cation channel modulatory subunit / Cyclic nucleotide-gated channel beta-1 / CNG channel beta-1 / Glutamic acid-rich protein / GARP


Mass: 155228.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q28181
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native CNGA1/CNGB1a channel / Type: COMPLEX / Details: purified from rod outer segments / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.356 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
9PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118084 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00515016
ELECTRON MICROSCOPYf_angle_d0.81420382
ELECTRON MICROSCOPYf_dihedral_angle_d12.7162023
ELECTRON MICROSCOPYf_chiral_restr0.0472303
ELECTRON MICROSCOPYf_plane_restr0.0052557

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