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- EMDB-63631: Structure of human TRPC5 bound with (-)-englerin A, class 2. -

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Basic information

Entry
Database: EMDB / ID: EMD-63631
TitleStructure of human TRPC5 bound with (-)-englerin A, class 2.
Map dataSharpened map of hTRPC5 with (-)-englerin A in the low calcium.
Sample
  • Complex: human TRPC5
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: ZINC ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (-)-englerin A
KeywordsTRPC5 / ion channel / (-)-englerin A / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / TRP channels / clathrin binding ...regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / negative regulation of dendrite morphogenesis / Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / inositol 1,4,5 trisphosphate binding / cation channel complex / actinin binding / TRP channels / clathrin binding / regulation of cytosolic calcium ion concentration / positive regulation of axon extension / calcium channel complex / positive regulation of neuron differentiation / calcium ion transmembrane transport / calcium channel activity / neuron differentiation / calcium ion transport / nervous system development / presynapse / actin binding / ATPase binding / growth cone / positive regulation of cytosolic calcium ion concentration / neuron apoptotic process / neuronal cell body / positive regulation of cell population proliferation / dendrite / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 5 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily ...Transient receptor potential channel, canonical 5 / Transient receptor ion channel domain / Transient receptor ion channel II / Transient receptor ion channel II / Transient receptor potential channel, canonical / Ankyrin repeat / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Short transient receptor potential channel 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsChen YK / Wei M / Chen L
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA0806504 China
National Natural Science Foundation of China (NSFC)32225027 China
CitationJournal: To Be Published
Title: Structure of human TRPC5 bound with (-)-englerin A, class 2.
Authors: Chen YK / Wei M / Chen L
History
DepositionMar 5, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63631.png

Downloads & links

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Map

FileDownload / File: emd_63631.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of hTRPC5 with (-)-englerin A in the low calcium.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 320 pix.
= 333.216 Å		1.04 Å/pix.
x 320 pix.
= 333.216 Å		1.04 Å/pix.
x 320 pix.
= 333.216 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0413 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.06
Minimum - Maximum-3.7756226 - 6.1681075
Average (Standard dev.)-0.0017197893 (±0.13121408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 333.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of hTRPC5 with (-)-englerin A in the low calcium.

Fileemd_63631_additional_1.map
AnnotationMap of hTRPC5 with (-)-englerin A in the low calcium.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of hTRPC5 with (-)-englerin A in the low calcium.

Fileemd_63631_half_map_1.map
AnnotationHalf map of hTRPC5 with (-)-englerin A in the low calcium.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of hTRPC5 with (-)-englerin A in the low calcium.

Fileemd_63631_half_map_2.map
AnnotationHalf map of hTRPC5 with (-)-englerin A in the low calcium.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human TRPC5

EntireName: human TRPC5
Components
  • Complex: human TRPC5
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: ZINC ION
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: (-)-englerin A

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Supramolecule #1: human TRPC5

SupramoleculeName: human TRPC5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Short transient receptor potential channel 5

MacromoleculeName: Short transient receptor potential channel 5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.221984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PEFMAQLYYK KVNYSPYRDR IPLQIVRAET ELSAEEKAFL NAVEKGDYAT VKQALQEAEI YYNVNINCMD PLGRSALLIA IENENLEIM ELLLNHSVYV GDALLYAIRK EVVGAVELLL SYRRPSGEKQ VPTLMMDTQF SEFTPDITPI MLAAHTNNYE I IKLLVQKR ...String:
PEFMAQLYYK KVNYSPYRDR IPLQIVRAET ELSAEEKAFL NAVEKGDYAT VKQALQEAEI YYNVNINCMD PLGRSALLIA IENENLEIM ELLLNHSVYV GDALLYAIRK EVVGAVELLL SYRRPSGEKQ VPTLMMDTQF SEFTPDITPI MLAAHTNNYE I IKLLVQKR VTIPRPHQIR CNCVECVSSS EVDSLRHSRS RLNIYKALAS PSLIALSSED PILTAFRLGW ELKELSKVEN EF KAEYEEL SQQCKLFAKD LLDQARSSRE LEIILNHRDD HSEELDPQKY HDLAKLKVAI KYHQKEFVAQ PNCQQLLATL WYD GFPGWR RKHWVVKLLT CMTIGFLFPM LSIAYLISPR SNLGLFIKKP FIKFICHTAS YLTFLFMLLL ASQHIVRTDL HVQG PPPTV VEWMILPWVL GFIWGEIKEM WDGGFTEYIH DWWNLMDFAM NSLYLATISL KIVAYVKYNG SRPREEWEMW HPTLI AEAL FAISNILSSL RLISLFTANS HLGPLQISLG RMLLDILKFL FIYCLVLLAF ANGLNQLYFY YETRAIDEPN NCKGIR CEK QNNAFSTLFE TLQSLFWSVF GLLNLYVTNV KARHEFTEFV GATMFGTYNV ISLVVLLNML IAMMNNSYQL IADHADI EW KFARTKLWMS YFDEGGTLPP PFNIIPSPKS FLYLGNWFNN TFCPKRDPDG RRRRRNLRSF TERNADSLIQ NQHYQEVI R NLVKRYVAAM IRNSKTHEGL TEENFKELKQ DISSFRYEVL DLLGNR

UniProtKB: Short transient receptor potential channel 5

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #4: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 4 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #6: (-)-englerin A

MacromoleculeName: (-)-englerin A / type: ligand / ID: 6 / Number of copies: 4 / Formula: A1L55
Molecular weightTheoretical: 442.545 Da

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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) / Number real images: 1311 / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109774
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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