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- PDB-7rh9: Cryo-EM structure of human rod CNGA1/B1 channel in apo state -

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Basic information

Entry
Database: PDB / ID: 7rh9
TitleCryo-EM structure of human rod CNGA1/B1 channel in apo state
Components
  • Cyclic nucleotide-gated cation channel beta-1
  • cGMP-gated cation channel alpha-1
KeywordsTRANSPORT PROTEIN / ion channel
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 / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment / VxPx cargo-targeting to cilium / Golgi-associated vesicle membrane / photoreceptor cell maintenance / retina homeostasis / photoreceptor outer segment membrane / ciliary membrane / sodium ion transport / transmembrane transporter complex / sodium channel activity / ligand-gated monoatomic ion channel activity / monoatomic cation transmembrane transport / cGMP binding / monoatomic cation transport / membrane depolarization / 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 / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cyclic nucleotide-gated channel alpha-1 / Cyclic nucleotide-gated channel beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsXue, J. / Han, Y. / Jiang, Y.
Funding support United States, 3items
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
Citation
Journal: Neuron / Year: 2022
Title: Structural mechanisms of assembly, permeation, gating, and pharmacology of native human rod CNG channel.
Authors: Jing Xue / Yan Han / Weizhong Zeng / Youxing Jiang /
Abstract: Mammalian cyclic nucleotide-gated (CNG) channels are nonselective cation channels activated by cGMP or cAMP and play essential roles in the signal transduction of the visual and olfactory sensory ...Mammalian cyclic nucleotide-gated (CNG) channels are nonselective cation channels activated by cGMP or cAMP and play essential roles in the signal transduction of the visual and olfactory sensory systems. CNGA1, the principal component of the CNG channel from rod photoreceptors, can by itself form a functional homotetrameric channel and has been used as the model system in the majority of rod CNG studies. However, the native rod CNG functions as a heterotetramer consisting of three A1 and one B1 subunits and exhibits different functional properties than the CNGA1 homomer. Here we present the functional analysis of human rod CNGA1/B1 heterotetramer and its cryo-EM structures in apo, cGMP-bound, cAMP-bound, and L-cis-Diltiazem-blocked states. These structures, with resolution ranging from 2.6 to 3.3 Å, elucidate the structural mechanisms underlying the 3:1 subunit stoichiometry, the asymmetrical gating upon cGMP activation, and the unique pharmacological property of the native rod CNG channel.
#1: Journal: 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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 3, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)284,9914
Polymers284,9914
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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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 / CNG1 / Cyclic ...Cyclic nucleotide-gated cation channel 1 / Cyclic nucleotide-gated channel alpha-1 / CNG1 / Cyclic nucleotide-gated channel / photoreceptor / Rod photoreceptor cGMP-gated channel subunit alpha


Mass: 64650.434 Da / Num. of mol.: 3 / Fragment: UNP residues 144-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNGA1, CNCG, CNCG1 / Production host: Homo sapiens (human) / References: UniProt: P29973
#2: Protein Cyclic nucleotide-gated cation channel beta-1 / Cyclic nucleotide-gated cation channel 4 / CNG channel 4 / CNG-4 / CNG4 / Cyclic nucleotide-gated ...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: 91039.305 Da / Num. of mol.: 1 / Fragment: UNP residues 454-1251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNGB1, CNCG2, CNCG3L, CNCG4, RCNC2 / Production host: Homo sapiens (human) / References: UniProt: Q14028
Has protein modificationN

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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: human rod Apo CNGA1/B1 channel in closed state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 687702 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315026
ELECTRON MICROSCOPYf_angle_d0.56520358
ELECTRON MICROSCOPYf_dihedral_angle_d4.0771991
ELECTRON MICROSCOPYf_chiral_restr0.0412276
ELECTRON MICROSCOPYf_plane_restr0.0062523

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