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- PDB-9upg: Cryo-EM structure of human olfactory CNGA2/A4/B1 in CaM-bound clo... -

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Basic information

Entry
Database: PDB / ID: 9upg
TitleCryo-EM structure of human olfactory CNGA2/A4/B1 in CaM-bound closed state
Components
  • Calmodulin-1
  • Cyclic nucleotide-gated channel alpha-2
  • Cyclic nucleotide-gated channel alpha-4
  • Cyclic nucleotide-gated channel beta-1
KeywordsMEMBRANE 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 / 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 / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / ciliary membrane / ligand-gated monoatomic ion channel activity / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / sodium ion transport / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / sodium channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / monoatomic cation transmembrane transport / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / cGMP binding / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / monoatomic cation transport / DARPP-32 events / membrane depolarization / catalytic complex / phototransduction / Smooth Muscle Contraction / photoreceptor outer segment / detection of calcium ion / regulation of cardiac muscle contraction / regulation of cytosolic calcium ion concentration / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / cAMP binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / calcium channel complex / visual perception / substantia nigra development / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / regulation of cytokinesis / VEGFR2 mediated vascular permeability / spindle microtubule
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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / 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: 2.87 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
A: Cyclic nucleotide-gated channel alpha-2
D: Cyclic nucleotide-gated channel alpha-4
C: Cyclic nucleotide-gated channel alpha-2
B: Cyclic nucleotide-gated channel beta-1
H: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,28311
Polymers375,0425
Non-polymers2406
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 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
#2: 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
#3: 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
#4: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Homo sapiens (human) / References: UniProt: P0DP23
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / 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 channel / Type: COMPLEX / Entity ID: #1-#4 / 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
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: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151054 / Symmetry type: POINT
RefinementHighest resolution: 2.87 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418290
ELECTRON MICROSCOPYf_angle_d0.5924759
ELECTRON MICROSCOPYf_dihedral_angle_d4.4442440
ELECTRON MICROSCOPYf_chiral_restr0.042767
ELECTRON MICROSCOPYf_plane_restr0.0053118

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