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- EMDB-51437: TRPC5 in complex with spin-labelled ligand SpinPico3 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51437
TitleTRPC5 in complex with spin-labelled ligand SpinPico3
Map data
Sample
  • Complex: TRPC5 homotetramer
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CALCIUM ION
  • Ligand: 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-(1,1,3,3-tetramethyl-2-oxidanyl-isoindol-5-yl)oxy-purine-2,6-dione
KeywordsMembrane protein / ion channel / inhibitor / non-covalent spin label / PROTEIN TRANSPORT
Function / homology
Function and homology information


regulation of membrane hyperpolarization / phosphatidylserine exposure on apoptotic cell surface / Role of second messengers in netrin-1 signaling / negative regulation of dendrite morphogenesis / 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 / Role of second messengers in netrin-1 signaling / negative regulation of dendrite morphogenesis / 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 / growth cone / positive regulation of cytosolic calcium ion concentration / ATPase binding / 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: 2.6 Å
AuthorsPorav SA / Bon RS / Hammond KLR
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P020208/1 United Kingdom
CitationJournal: To Be Published
Title: Non-covalent spin labelling of TRPC5 ion channels enables EPR studies of protein-ligand interactions
Authors: Johnson AJ / Porav SA / Hammond KLR / Shah A / Hassane EM / Pask CM / Muench SP / Wilson AJ / Pilotas C / Bon RS
History
DepositionAug 27, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51437.png

Downloads & links

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Map

FileDownload / File: emd_51437.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-1.373946 - 1.8364401
Average (Standard dev.)0.0034996362 (±0.03760758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51437_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Resolve CryoEM map

Fileemd_51437_additional_1.map
AnnotationResolve CryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51437_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51437_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRPC5 homotetramer

EntireName: TRPC5 homotetramer
Components
  • Complex: TRPC5 homotetramer
    • Protein or peptide: Short transient receptor potential channel 5
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: CALCIUM ION
  • Ligand: 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-(1,1,3,3-tetramethyl-2-oxidanyl-isoindol-5-yl)oxy-purine-2,6-dione

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Supramolecule #1: TRPC5 homotetramer

SupramoleculeName: TRPC5 homotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 480 KDa

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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: 89.00982 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLNAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR RPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI ...String:
MAQLYYKKVN YSPYRDRIPL QIVRAETELS AEEKAFLNAV EKGDYATVKQ ALQEAEIYYN VNINCMDPLG RSALLIAIEN ENLEIMELL LNHSVYVGDA LLYAIRKEVV GAVELLLSYR RPSGEKQVPT LMMDTQFSEF TPDITPIMLA AHTNNYEIIK L LVQKRVTI PRPHQIRCNC VECVSSSEVD SLRHSRSRLN IYKALASPSL IALSSEDPIL TAFRLGWELK ELSKVENEFK AE YEELSQQ CKLFAKDLLD QARSSRELEI ILNHRDDHSE ELDPQKYHDL AKLKVAIKYH QKEFVAQPNC QQLLATLWYD GFP GWRRKH WVVKLLTCMT IGFLFPMLSI AYLISPRSNL GLFIKKPFIK FICHTASYLT FLFMLLLASQ HIVRTDLHVQ GPPP TVVEW MILPWVLGFI WGEIKEMWDG GFTEYIHDWW NLMDFAMNSL YLATISLKIM AYVKYNGSRP REEWEMWHPT LIAEA LFAI SNILSSLRLI SLFTANSHLG PLQISLGRML LDILKFLFIY CLVLLAFANG LNQLYFYYET RAIDEPNNCK GIRCEK QNN AFSTLFETLQ SLFWSVFGLL NLYVTNVKAR HEFTEFVGAT MFGTYNVISL VVLLNMLIAM MNNSYQLIAD HADIEWK FA RTKLWMSYFD EGGTLPPPFN IIPSPKSFLY LGNWFNNTFC PKRDPDGRRR RRNLRSFTER NADSLIQNQH YQEVIRNL V KRYVAAMIRN SKTHEGLTEE NFKELKQDIS SFRYEVLDLL GNRK

UniProtKB: Short transient receptor potential channel 5

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-(1,1,3...

MacromoleculeName: 7-[(4-chlorophenyl)methyl]-3-methyl-1-(3-oxidanylpropyl)-8-(1,1,3,3-tetramethyl-2-oxidanyl-isoindol-5-yl)oxy-purine-2,6-dione
type: ligand / ID: 4 / Number of copies: 4 / Formula: A1IMP
Molecular weightTheoretical: 554.037 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

Concentration0.9 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 mMNaClSodium Chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 35.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 30.0 µm / Nominal defocus min: 7.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107035
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9gl6:
TRPC5 in complex with spin-labelled ligand SpinPico3

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