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- PDB-7rhs: Cryo-EM structure of apo-state of human CNGA3/CNGB3 channel -

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Basic information

Entry
Database: PDB / ID: 7rhs
TitleCryo-EM structure of apo-state of human CNGA3/CNGB3 channel
Components
  • Cyclic nucleotide-gated cation channel alpha-3
  • Cyclic nucleotide-gated cation channel beta-3
KeywordsTRANSPORT PROTEIN / cone / CNG channel / cGMP
Function / homology
Function and homology information


inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / transmembrane transporter complex / axon initial segment / ligand-gated monoatomic ion channel activity / myosin binding / sodium channel activity / monoatomic cation transmembrane transport ...inorganic cation import across plasma membrane / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / intracellularly cAMP-activated cation channel activity / transmembrane transporter complex / axon initial segment / ligand-gated monoatomic ion channel activity / myosin binding / sodium channel activity / monoatomic cation transmembrane transport / cGMP binding / response to magnesium ion / monoatomic cation transport / response to cAMP / glial cell projection / photoreceptor outer segment / visual perception / calcium channel activity / perikaryon / cadherin binding / dendrite / protein-containing complex binding / signal transduction / 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-3 / Cyclic nucleotide-gated channel beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZheng, X. / Yang, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM085234 United States
National Institutes of Health/National Eye Institute (NIH/NEI)RO1EY027800 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structure of the human cone photoreceptor cyclic nucleotide-gated channel.
Authors: Xiangdong Zheng / Zhengshan Hu / Huan Li / Jian Yang /
Abstract: Cyclic nucleotide-gated (CNG) channels transduce light-induced chemical signals into electrical signals in retinal cone and rod photoreceptors. Structures of native CNG channels, which are ...Cyclic nucleotide-gated (CNG) channels transduce light-induced chemical signals into electrical signals in retinal cone and rod photoreceptors. Structures of native CNG channels, which are heterotetramers formed by CNGA and CNGB subunits, have not been obtained. In the present study, we report a high-resolution cryo-electron microscopy structure of the human cone CNG channel in the apo closed state. The channel contains three CNGA3 and one CNGB3 subunits. Arg403 in the pore helix of CNGB3 projects into an asymmetric selectivity filter and forms hydrogen bonds with two pore-lining backbone carbonyl oxygens. Arg442 in S6 of CNGB3 protrudes into and occludes the pore below the hydrophobic cavity gate previously observed in homotetrameric CNGA channels. It is interesting that Arg403Gln is a disease mutation, and Arg442 is replaced by glutamine in some animal species with dichromatic or monochromatic vision. These and other unique structural features and the disease link conferred by CNGB3 indicate a critical role of CNGB3 in shaping cone photoresponses.
History
DepositionJul 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update
Revision 1.1May 28, 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 / Item: _em_admin.last_update

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Cyclic nucleotide-gated cation channel alpha-3
B: Cyclic nucleotide-gated cation channel alpha-3
C: Cyclic nucleotide-gated cation channel alpha-3
D: Cyclic nucleotide-gated cation channel beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,8378
Polymers336,1504
Non-polymers6874
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22080 Å2
ΔGint-127 kcal/mol
Surface area81060 Å2

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Components

#1: Protein Cyclic nucleotide-gated cation channel alpha-3 / Cone photoreceptor cGMP-gated channel subunit alpha / Cyclic nucleotide-gated channel alpha-3 / CNG ...Cone photoreceptor cGMP-gated channel subunit alpha / Cyclic nucleotide-gated channel alpha-3 / CNG channel alpha-3 / CNG-3 / CNG3


Mass: 80233.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNGA3, CNCG3 / Production host: Homo sapiens (human) / References: UniProt: Q16281
#2: Protein Cyclic nucleotide-gated cation channel beta-3 / Cone photoreceptor cGMP-gated channel subunit beta / Cyclic nucleotide-gated cation channel ...Cone photoreceptor cGMP-gated channel subunit beta / Cyclic nucleotide-gated cation channel modulatory subunit / Cyclic nucleotide-gated channel beta-3 / CNG channel beta-3


Mass: 95450.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNGB3 / Production host: Homo sapiens (human) / References: UniProt: Q9NQW8
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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 human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.58
SpecimenConc.: 1.5 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: OTHER
Image recordingAverage exposure time: 2 sec. / Electron dose: 57.63 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
2Leginonimage acquisition
4GctfCTF correction
7Cootmodel fitting
8UCSF Chimeramodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12RELIONclassification
13cryoSPARC3D reconstruction
14UCSF Chimeramodel refinement
15PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205492 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00615093
ELECTRON MICROSCOPYf_angle_d0.89120471
ELECTRON MICROSCOPYf_dihedral_angle_d13.6588934
ELECTRON MICROSCOPYf_chiral_restr0.0562330
ELECTRON MICROSCOPYf_plane_restr0.0082537

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