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- EMDB-37720: Cryo-EM structure of the human TRPC4 in lipid nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-37720
TitleCryo-EM structure of the human TRPC4 in lipid nanodiscs
Map data
Sample
  • Complex: Structure of a TRP channel
    • Protein or peptide: Short transient receptor potential channel 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
Keywordstransient receptor potential / METAL TRANSPORT
Function / homology
Function and homology information


Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / gamma-aminobutyric acid secretion / cation channel complex / inositol 1,4,5 trisphosphate binding / calcium ion import / TRP channels / cortical cytoskeleton / oligodendrocyte differentiation / regulation of cytosolic calcium ion concentration ...Role of second messengers in netrin-1 signaling / store-operated calcium channel activity / gamma-aminobutyric acid secretion / cation channel complex / inositol 1,4,5 trisphosphate binding / calcium ion import / TRP channels / cortical cytoskeleton / oligodendrocyte differentiation / regulation of cytosolic calcium ion concentration / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / caveola / beta-catenin binding / calcium ion transport / basolateral plasma membrane / cadherin binding / cell surface / plasma membrane
Similarity search - Function
Transient receptor potential channel, canonical 4 / 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 repeat region circular profile. / Ankyrin repeat profile. / ankyrin repeats ...Transient receptor potential channel, canonical 4 / 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 repeat region circular profile. / Ankyrin repeat 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsWon J / Jeong H / Lee HH
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
Other privateSSTF-BA2101-13 Korea, Republic Of
CitationJournal: To Be Published
Title: Structure of a TRP channel
Authors: Won J / Jeong H / Lee HH
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37720.png

Downloads & links

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Map

FileDownload / File: emd_37720.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.72 Å		1.07 Å/pix.
x 320 pix.
= 342.72 Å		1.07 Å/pix.
x 320 pix.
= 342.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.6441231 - 2.577268
Average (Standard dev.)0.00018096252 (±0.07464837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37720_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_37720_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 : Structure of a TRP channel

EntireName: Structure of a TRP channel
Components
  • Complex: Structure of a TRP channel
    • Protein or peptide: Short transient receptor potential channel 4
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

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Supramolecule #1: Structure of a TRP channel

SupramoleculeName: Structure of a TRP channel / 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 4

MacromoleculeName: Short transient receptor potential channel 4 / type: protein_or_peptide / ID: 1 / Details: SRASTVPRARDPPVATLEVLFQ (894-915), linker / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 105.157977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQFYYKRNV NAPYRDRIPL RIVRAESELS PSEKAYLNAV EKGDYASVKK SLEEAEIYFK ININCIDPLG RTALLIAIEN ENLELIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSEF TPDITPIILA AHTNNYEIIK L LVQKGVSV ...String:
MAQFYYKRNV NAPYRDRIPL RIVRAESELS PSEKAYLNAV EKGDYASVKK SLEEAEIYFK ININCIDPLG RTALLIAIEN ENLELIELL LSFNVYVGDA LLHAIRKEVV GAVELLLNHK KPSGEKQVPP ILLDKQFSEF TPDITPIILA AHTNNYEIIK L LVQKGVSV PRPHEVRCNC VECVSSSDVD SLRHSRSRLN IYKALASPSL IALSSEDPFL TAFQLSWELQ ELSKVENEFK SE YEELSRQ CKQFAKDLLD QTRSSRELEI ILNYRDDNSL IEEQSGNDLA RLKLAIKYRQ KEFVAQPNCQ QLLASRWYDE FPG WRRRHW AVKMVTCFII GLLFPVFSVC YLIAPKSPLG LFIRKPFIKF ICHTASYLTF LFLLLLASQH IDRSDLNRQG PPPT IVEWM ILPWVLGFIW GEIKQMWDGG LQDYIHDWWN LMDFVMNSLY LATISLKIVA FVKYSALNPR ESWDMWHPTL VAEAL FAIA NIFSSLRLIS LFTANSHLGP LQISLGRMLL DILKFLFIYC LVLLAFANGL NQLYFYYEET KGLTCKGIRC EKQNNA FST LFETLQSLFW SIFGLINLYV TNVKAQHEFT EFVGATMFGT YNVISLVVLL NMLIAMMNNS YQLIADHADI EWKFART KL WMSYFEEGGT LPTPFNVIPS PKSLWYLIKW IWTHLCKKKM RRKPESFGTI GRRAADNLRR HHQYQEVMRN LVKRYVAA M IRDAKTEEGL TEENFKELKQ DISSFRFEVL GLLRGSKLST IQSANASKES SNSADSDEKS DSEEEVARQQ AAGPLERNI QLESRGLASR GDLSIPGLSE QCVLVDHRER NTDTLGLQVG KRVCPFKSEK VVVEDTVPII PKEKHAKEED SSIDYDLNLP DTVTHEDYV TTRLSRASTV PRARDPPVAT LEVLFQ

UniProtKB: Short transient receptor potential channel 4

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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: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: CALCIUM ION

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

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Macromolecule #5: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE

MacromoleculeName: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
type: ligand / ID: 5 / Number of copies: 4 / Formula: LPP
Molecular weightTheoretical: 648.891 Da
Chemical component information

ChemComp-LPP:
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / phospholipid*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5z96

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 118370
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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