6BWI | pdb_00006bwi

3.7 angstrom cryoEM structure of full length human TRPM4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6BWI

This is version 1.5 of the entry. See complete history

Literature

Structure of full-length human TRPM4.

Duan, J.Li, Z.Li, J.Santa-Cruz, A.Sanchez-Martinez, S.Zhang, J.Clapham, D.E.

(2018) Proc Natl Acad Sci U S A 115: 2377-2382

  • DOI: https://doi.org/10.1073/pnas.1722038115
  • Primary Citation Related Structures: 
    6BWI

  • PubMed Abstract: 

    Transient receptor potential melastatin subfamily member 4 (TRPM4) is a widely distributed, calcium-activated, monovalent-selective cation channel. Mutations in human TRPM4 (hTRPM4) result in progressive familial heart block. Here, we report the electron cryomicroscopy structure of hTRPM4 in a closed, Na + -bound, apo state at pH 7.5 to an overall resolution of 3.7 Å. Five partially hydrated sodium ions are proposed to occupy the center of the conduction pore and the entrance to the coiled-coil domain. We identify an upper gate in the selectivity filter and a lower gate at the entrance to the cytoplasmic coiled-coil domain. Intramolecular interactions exist between the TRP domain and the S4-S5 linker, N-terminal domain, and N and C termini. Finally, we identify aromatic interactions via π-π bonds and cation-π bonds, glycosylation at an N-linked extracellular site, a pore-loop disulfide bond, and 24 lipid binding sites. We compare and contrast this structure with other TRP channels and discuss potential mechanisms of regulation and gating of human full-length TRPM4.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, Ashburn, VA 20147.

Macromolecule Content 

  • Total Structure Weight: 430.78 kDa 
  • Atom Count: 23,491 
  • Modeled Residue Count: 3,264 
  • Deposited Residue Count: 3,908 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily M member 4
A, B, C, D
977Homo sapiensMutation(s): 0 
Gene Names: TRPM4LTRPC4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TD43 (Homo sapiens)
Explore Q8TD43 
Go to UniProtKB:  Q8TD43
PHAROS:  Q8TD43
GTEx:  ENSG00000130529 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TD43
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01

Query on Y01



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
DA [auth D]
EA [auth D]
FA [auth D]
AA [auth C],
BA [auth C],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
X [auth C],
Y [auth C],
Z [auth C]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CA [auth C],
KA [auth D],
N [auth A],
W [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
O [auth B],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2025-06-04
    Changes: Data collection