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- EMDB-63868: Structure of hTRPC3 in complex with Nb1-94 at 2.25 angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-63868
TitleStructure of hTRPC3 in complex with Nb1-94 at 2.25 angstrom
Map data
Sample
  • Complex: TRPC3 tetramer combined with Nb1-94
    • Protein or peptide: Short transient receptor potential channel 3
    • Protein or peptide: Nb1-94
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
  • Ligand: water
KeywordsTRPC3 / DAG / Nb1-94 / nanobody / METAL TRANSPORT
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 / cation channel complex / calcium-activated cation channel activity / 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 / cation channel complex / calcium-activated cation channel activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.25 Å
AuthorsChen L / Chen Y / Zang J
Funding support China, 2 items
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, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63868.png

Downloads & links

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Map

FileDownload / File: emd_63868.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 399.84 Å		0.83 Å/pix.
x 480 pix.
= 399.84 Å		0.83 Å/pix.
x 480 pix.
= 399.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.0373116 - 5.355411
Average (Standard dev.)-0.0027781045 (±0.09537556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 399.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63868_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63868_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63868_half_map_2.map
Projections & Slices
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Sample components

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Entire : TRPC3 tetramer combined with Nb1-94

EntireName: TRPC3 tetramer combined with Nb1-94
Components
  • Complex: TRPC3 tetramer combined with Nb1-94
    • Protein or peptide: Short transient receptor potential channel 3
    • Protein or peptide: Nb1-94
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
  • Ligand: water

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Supramolecule #1: TRPC3 tetramer combined with Nb1-94

SupramoleculeName: TRPC3 tetramer combined with Nb1-94 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Short transient receptor potential channel 3

MacromoleculeName: Short transient receptor potential channel 3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.118227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MREKGRRQAV RGPAFMFNDR GTSLTAEEER FLDAAEYGNI PVVRKMLEES KTLNVNCVDY MGQNALQLAV GNEHLEVTEL LLKKENLAR IGDALLLAIS KGYVRIVEAI LNHPGFAASK RLTLSPCEQE LQDDDFYAYD EDGTRFSPDI TPIILAAHCQ K YEVVHMLL ...String:
MREKGRRQAV RGPAFMFNDR GTSLTAEEER FLDAAEYGNI PVVRKMLEES KTLNVNCVDY MGQNALQLAV GNEHLEVTEL LLKKENLAR IGDALLLAIS KGYVRIVEAI LNHPGFAASK RLTLSPCEQE LQDDDFYAYD EDGTRFSPDI TPIILAAHCQ K YEVVHMLL MKGARIERPH DYFCKCGDCM EKQRHDSFSH SRSRINAYKG LASPAYLSLS SEDPVLTALE LSNELAKLAN IE KEFKNDY RKLSMQCKDF VVGVLDLCRD SEEVEAILNG DLESAEPLEV HRHKASLSRV KLAIKYEVKK FVAHPNCQQQ LLT IWYENL SGLREQTIAI KCLVVLVVAL GLPFLAIGYW IAPCSRLGKI LRSPFMKFVA HAASFIIFLG LLVFNASDRF EGIT TLPNI TVTDYPKQIF RVKTTQFTWT EMLIMVWVLG MMWSECKELW LEGPREYILQ LWNVLDFGML SIFIAAFTAR FLAFL QATK AQQYVDSYVQ ESDLSEVTLP PEIQYFTYAR DKWLPSDPQI ISEGLYAIAV VLSFSRIAYI LPANESFGPL QISLGR TVK DIFKFMVLFI MVFFAFMIGM FILYSYYLGA KVNAAFTTVE ESFKTLFWSI FGLSEVTSVV LKYDHKFIEN IGYVLYG IY NVTMVVVLLN MLIAMINSSY QEIEDDSDVE WKFARSKLWL SYFDDGKTLP PPFSLVPSPK SFVYFIMRIV NFPKCRRR R LQKDIEMGMG NSKSRLNLFT QSNSRVFESH SFNSILNQPT RYQQIMKRLI KRYVLKAQVD KENDEVNEGE LKEIKQDIS SLRYELLEDK SQATEELAIL IHKLSEKLNP SMLRCE

UniProtKB: Short transient receptor potential channel 3

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Macromolecule #2: Nb1-94

MacromoleculeName: Nb1-94 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Camelus (mammal)
Molecular weightTheoretical: 14.058547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG SVQSGGSLRL SCAASGYTYS YSGYCMGWFR QAPGKEREGV ATIDGAGNTK YADSVKGRFT ISRDNAKKTL YLQMNSLKP EDTAMYYCAA RVYSYSSDVD CRPSFTTRFP YSGQGTQVTV

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec...

MacromoleculeName: [(2~{S})-2-[(~{E})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] octadec-9-enoate
type: ligand / ID: 5 / Number of copies: 4 / Formula: A1L5I
Molecular weightTheoretical: 620.986 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 254083
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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