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- PDB-8ev9: Cryo-EM structure of cGMP bound truncated human CNGA3/CNGB3 chann... -

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Basic information

Entry
Database: PDB / ID: 8ev9
TitleCryo-EM structure of cGMP bound truncated human CNGA3/CNGB3 channel in lipid nanodisc, transition state 1
Components
  • Cyclic nucleotide-gated cation channel alpha-3
  • Cyclic nucleotide-gated cation channel beta-3
KeywordsMEMBRANE PROTEIN / CNGA3 / CNGB3 / ligand-bound
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 / axon initial segment / sodium channel activity / myosin binding / monoatomic cation transmembrane transport / monoatomic cation transport / glial cell projection ...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 / axon initial segment / sodium channel activity / myosin binding / monoatomic cation transmembrane transport / monoatomic cation transport / glial cell projection / cGMP binding / response to magnesium ion / ligand-gated monoatomic ion channel activity / photoreceptor outer segment / transmembrane transporter complex / response to cAMP / 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 GUANOSINE MONOPHOSPHATE / 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: 3.33 Å
AuthorsHu, Z. / Yang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI) United States
CitationJournal: Nat Commun / Year: 2023
Title: Conformational trajectory of allosteric gating of the human cone photoreceptor cyclic nucleotide-gated channel.
Authors: Zhengshan Hu / Xiangdong Zheng / Jian Yang /
Abstract: Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide- ...Cyclic nucleotide-gated (CNG) channels transduce chemical signals into electrical signals in sensory receptors and neurons. They are activated by cGMP or cAMP, which bind to the cyclic nucleotide-binding domain (CNBD) to open a gate located 50-60 Å away in the central cavity. Structures of closed and open vertebrate CNG channels have been solved, but the conformational landscape of this allosteric gating remains to be elucidated and enriched. Here, we report structures of the cGMP-activated human cone photoreceptor CNGA3/CNGB3 channel in closed, intermediate, pre-open and open states in detergent or lipid nanodisc, all with fully bound cGMP. The pre-open and open states are obtained only in the lipid nanodisc, suggesting a critical role of lipids in tuning the energetic landscape of CNGA3/CNGB3 activation. The different states exhibit subunit-unique, incremental and distinct conformational rearrangements that originate in the CNBD, propagate through the gating ring to the transmembrane domain, and gradually open the S6 cavity gate. Our work illustrates a spatial conformational-change wave of allosteric gating of a vertebrate CNG channel by its natural ligand and provides an expanded framework for studying CNG properties and channelopathy.
History
DepositionOct 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)276,89011
Polymers274,8464
Non-polymers2,0447
Water00
1


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

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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: 63402.836 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: 84637.156 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
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-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
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: Truncated human cone photoreceptor heterotetrameric CNG channel CNGA3/CNGB3 in complex with cGMP in lipid nanodisc
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8.58
SpecimenEmbedding 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 / Nominal defocus max: 1500 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 61.05 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304034 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 68.16 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009615013
ELECTRON MICROSCOPYf_angle_d0.997820381
ELECTRON MICROSCOPYf_chiral_restr0.06332319
ELECTRON MICROSCOPYf_plane_restr0.00832504
ELECTRON MICROSCOPYf_dihedral_angle_d26.4755461

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