[English] 日本語
Yorodumi
- EMDB-37720: Cryo-EM structure of the human TRPC4 in lipid nanodiscs -

+
Open data


ID or keywords:

Loading...

-
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 / gamma-aminobutyric acid secretion / store-operated calcium channel activity / 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 / gamma-aminobutyric acid secretion / store-operated calcium channel activity / 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 / beta-catenin binding / caveola / calcium channel activity / calcium ion transmembrane transport / 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 profile. / Ankyrin repeat region circular 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 profile. / 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 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: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM structure of the heteromeric TRPC1/TRPC4 channel.
Authors: Jongdae Won / Jinhyeong Kim / Jinsung Kim / Juyeon Ko / Christine Haewon Park / Byeongseok Jeong / Sang-Eun Lee / Hyeongseop Jeong / Sun-Hong Kim / Hyunwoo Park / Insuk So / Hyung Ho Lee /
Abstract: Transient receptor potential (TRP) ion channels have a crucial role as cellular sensors, mediating diverse physical and chemical stimuli. The formation of heteromeric structures expands the ...Transient receptor potential (TRP) ion channels have a crucial role as cellular sensors, mediating diverse physical and chemical stimuli. The formation of heteromeric structures expands the functionality of TRP channels; however, their molecular architecture remains largely unknown. Here we present the cryo-electron microscopy structures of the human TRPC1/TRPC4 heteromer in the apo and antagonist-bound states, both consisting of one TRPC1 subunit and three TRPC4 subunits. The heteromer structure reveals a distinct ion-conduction pathway, including an asymmetrically constricted selectivity filter and an asymmetric lower gate, primarily attributed to the incorporation of TRPC1. Through a structure-guided electrophysiological assay, we show that both the selectivity filter and the lower part of the S6 helix participate in deciding overall preference for permeating monovalent cations. Moreover, we reveal that the introduction of one lysine residue of TRPC1 into the tetrameric central cavity is enough to render one of the most important functional consequences of TRPC heteromerization: reduced calcium permeability. Our results establish a framework for addressing the structure-function relationship of the heteromeric TRP channels.
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37720.png

Downloads & links

-
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 °

-
Supplemental data

-
Half map: #2

Fileemd_37720_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37720_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
Macromolecule #3: ZINC ION

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

-
Macromolecule #4: CALCIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more