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- PDB-9u5c: Structure of hTRPC3 in complex with Nb1-94 at 2.25 angstrom -

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Basic information

Entry
Database: PDB / ID: 9u5c
TitleStructure of hTRPC3 in complex with Nb1-94 at 2.25 angstrom
Components
  • Nb1-94
  • Short transient receptor potential channel 3
KeywordsMETAL TRANSPORT / TRPC3 / DAG / Nb1-94 / nanobody
Function / homology
Function and homology information


positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / cation channel complex / TRP channels / response to ATP ...positive regulation of cardiac muscle hypertrophy in response to stress / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / Effects of PIP2 hydrolysis / Elevation of cytosolic Ca2+ levels / inositol 1,4,5 trisphosphate binding / calcium-activated cation channel activity / cation channel complex / TRP channels / response to ATP / positive regulation of calcium ion transport into cytosol / phototransduction / regulation of cytosolic calcium ion concentration / single fertilization / MECP2 regulates neuronal receptors and channels / response to calcium ion / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / metal ion binding / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 3 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / Short transient receptor potential channel 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Camelus (mammal)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsChen, L. / Chen, Y. / Zang, J.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303000 China
National Natural Science Foundation of China (NSFC)32225027 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanism of the agonist binding on human TRPC3 channel.
Authors: Yikun Chen / Jiahe Zang / Wenjun Guo / Jiaxuan Xu / Miao Wei / Li Quan / Min Zhu / Xiaole Zhao / Hailin Peng / Yakun Wan / Lei Chen /
Abstract: TRPC3/6/7 channels are cation channels that are directly activated by the second messenger diacylglycerol (DAG). These channels play crucial physiological roles and are implicated in various disease ...TRPC3/6/7 channels are cation channels that are directly activated by the second messenger diacylglycerol (DAG). These channels play crucial physiological roles and are implicated in various disease conditions; however, the binding mechanism of DAG to these channels remains incompletely understood. In this study, we present the structures of human TRPC3 in complex with DAG or synthetic activators, 4n and GSK1702934A. The structural analysis reveals that DAG binds at the L2 site, located near the pore on the extracellular side of TRPC3. Functional assays confirmed that the L2 site serves as the activating site for DAG. Notably, both 4n and GSK1702934A competitively bind to the same site, facilitating channel activation. Moreover, based on the pharmacophore identified from the DAG-bound structure, we found that monoacylglycerols (MAGs) are endogenous activators of TRPC3/6/7 channels, providing new insights into their regulatory mechanisms.
History
DepositionMar 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short transient receptor potential channel 3
B: Nb1-94
C: Short transient receptor potential channel 3
D: Nb1-94
E: Short transient receptor potential channel 3
F: Nb1-94
G: Short transient receptor potential channel 3
H: Nb1-94
hetero molecules


Theoretical massNumber of molelcules
Total (without water)443,77324
Polymers440,7078
Non-polymers3,06616
Water57632
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

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Short transient receptor potential channel 3 / TrpC3 / Transient receptor protein 3 / hTrp3


Mass: 96118.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRPC3, TRP3 / Production host: Homo sapiens (human) / References: UniProt: Q13507
#2: Protein
Nb1-94


Mass: 14058.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus (mammal) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 48 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-A1L5I / [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate


Mass: 620.986 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H72O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

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: TRPC3 tetramer combined with Nb1-94 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254083 / Symmetry type: POINT

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