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- PDB-7rhh: Cryo-EM structure of human rod CNGA1/B1 channel in cGMP-bound ope... -

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Basic information

Entry
Database: PDB / ID: 7rhh
TitleCryo-EM structure of human rod CNGA1/B1 channel in cGMP-bound openI 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 / protein localization to organelle / intracellular cyclic nucleotide activated cation channel complex / detection of light stimulus involved in visual perception / intracellularly cGMP-activated cation channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant ...olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / intracellular cyclic nucleotide activated cation channel complex / detection of light stimulus involved in visual perception / intracellularly cGMP-activated cation channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / intracellularly cAMP-activated cation channel activity / Golgi-associated vesicle membrane / photoreceptor cell maintenance / retina homeostasis / sodium channel activity / ciliary membrane / photoreceptor outer segment membrane / sodium ion transport / monoatomic cation transmembrane transport / monoatomic cation transport / phototransduction / membrane depolarization / cGMP binding / ligand-gated monoatomic ion channel activity / photoreceptor outer segment / transmembrane transporter complex / cAMP binding / regulation of cytosolic calcium ion concentration / visual perception / potassium ion transport / Olfactory Signaling Pathway / calcium channel activity / Activation of the phototransduction cascade / terminal bouton / calcium ion transport / Inactivation, recovery and regulation of the phototransduction cascade / sensory perception of smell / 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-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 GUANOSINE MONOPHOSPHATE / 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: 3.31 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
CitationJournal: 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.
History
DepositionJul 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)286,3718
Polymers284,9914
Non-polymers1,3814
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
#3: Chemical
ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O7P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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 CNGA1/B1 channel in cGMP-bound openI state / Type: COMPLEX / Entity ID: #1-#2 / 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
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54022 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315076
ELECTRON MICROSCOPYf_angle_d0.56820446
ELECTRON MICROSCOPYf_dihedral_angle_d3.9591991
ELECTRON MICROSCOPYf_chiral_restr0.0422282
ELECTRON MICROSCOPYf_plane_restr0.0052518

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