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- PDB-9upf: Cryo-EM structure of human olfactory CNG channel in cAMP-bound op... -

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Basic information

Entry
Database: PDB / ID: 9upf
TitleCryo-EM structure of human olfactory CNG channel in cAMP-bound open state
Components
  • Cyclic nucleotide-gated channel alpha-2
  • Cyclic nucleotide-gated channel alpha-4
  • Cyclic nucleotide-gated channel beta-1
KeywordsMEMBRANE PROTEIN / Ion Channels
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 / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment ...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 / intracellularly cAMP-activated cation channel activity / rod photoreceptor outer segment / VxPx cargo-targeting to cilium / detection of light stimulus involved in visual perception / Golgi-associated vesicle membrane / transmembrane transporter complex / photoreceptor cell maintenance / retina homeostasis / ligand-gated monoatomic ion channel activity / ciliary membrane / sodium ion transport / sodium channel activity / monoatomic cation transmembrane transport / cGMP binding / monoatomic cation transport / membrane depolarization / phototransduction / photoreceptor outer segment / regulation of cytosolic calcium ion concentration / cAMP binding / visual perception / potassium ion transport / calcium channel activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / terminal bouton / calcium ion transport / sensory perception of smell / Inactivation, recovery and regulation of the phototransduction cascade / calmodulin binding / G protein-coupled receptor signaling pathway / 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 / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic nucleotide-gated channel beta-1 / Cyclic nucleotide-gated channel alpha-2 / Cyclic nucleotide-gated channel alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsXue, J. / Jiang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Structural mechanisms underlying assembly, gating, and calmodulin inhibition of olfactory CNG channels
Authors: Xue, J. / Jiang, Y.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cyclic nucleotide-gated channel beta-1
A: Cyclic nucleotide-gated channel alpha-2
D: Cyclic nucleotide-gated channel alpha-4
C: Cyclic nucleotide-gated channel alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,58710
Polymers358,1904
Non-polymers1,3976
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Cyclic nucleotide-gated channel beta-1 / CNG channel beta-1 / Cyclic nucleotide-gated cation channel 4 / CNG channel 4 / CNG-4 / CNG4 / ...CNG channel beta-1 / 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 / Glutamic acid-rich protein / GARP


Mass: 139831.812 Da / Num. of mol.: 1
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
#2: Protein Cyclic nucleotide-gated channel alpha-2 / CNG channel alpha-2 / CNG-2 / CNG2 / Olfactory cyclic nucleotide-gated channel subunit 1 / OCNC1


Mass: 76144.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNGA2, CNCA, CNCA1, CNCG2 / Production host: Homo sapiens (human) / References: UniProt: Q16280
#3: Protein Cyclic nucleotide-gated channel alpha-4 / CNG channel alpha-4 / CNGa4 / Olfactory cyclic nucleotide-gated channel subunit 2 / OCNC2


Mass: 66069.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNGA4 / Production host: Homo sapiens (human) / References: UniProt: Q8IV77
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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 olfactory CNG channels / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI SPHERA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43707 / Symmetry type: POINT
RefinementHighest resolution: 3.59 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314950
ELECTRON MICROSCOPYf_angle_d0.76320290
ELECTRON MICROSCOPYf_dihedral_angle_d11.5072029
ELECTRON MICROSCOPYf_chiral_restr0.0422261
ELECTRON MICROSCOPYf_plane_restr0.0052504

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