5TJB

I-II linker of TRPML1 channel at pH 4.5

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 
  • Membrane Protein: Yes  mpstruc

  • Deposited: 2016-10-04 Released: 2017-01-25 
  • Deposition Author(s): Li, M., Zhang, W.K., Benvin, N.M., Zhou, X., Su, D., Li, H., Wang, S., Michailidis, I.E., Tong, L., Li, X., Yang, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Basic Research Program of China (973 Program), National Natural Science Foundation of China (NSFC), Top Talents Program of Yunnan Province, High-level Overseas Talents of Yunnan Province, China Youth 1000-Talent Program of the State Council of China, Beijing Advanced Innovation Center for Structural Biology

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structural basis of dual Ca(2+)/pH regulation of the endolysosomal TRPML1 channel.

Li, M.Zhang, W.K.Benvin, N.M.Zhou, X.Su, D.Li, H.Wang, S.Michailidis, I.E.Tong, L.Li, X.Yang, J.

(2017) Nat Struct Mol Biol 24: 205-213

  • DOI: https://doi.org/10.1038/nsmb.3362
  • Primary Citation of Related Structures:  
    5TJA, 5TJB, 5TJC

  • PubMed Abstract: 

    The activities of organellar ion channels are often regulated by Ca 2+ and H + , which are present in high concentrations in many organelles. Here we report a structural element critical for dual Ca 2+ /pH regulation of TRPML1, a Ca 2+ -release channel crucial for endolysosomal function. TRPML1 mutations cause mucolipidosis type IV (MLIV), a severe lysosomal storage disorder characterized by neurodegeneration, mental retardation and blindness. We obtained crystal structures of the 213-residue luminal domain of human TRPML1 containing three missense MLIV-causing mutations. This domain forms a tetramer with a highly electronegative central pore formed by a novel luminal pore loop. Cysteine cross-linking and cryo-EM analyses confirmed that this architecture occurs in the full-length channel. Structure-function studies demonstrated that Ca 2+ and H + interact with the luminal pore and exert physiologically important regulation. The MLIV-causing mutations disrupt the luminal-domain structure and cause TRPML1 mislocalization. Our study reveals the structural underpinnings of TRPML1's regulation, assembly and pathogenesis.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucolipin-1223Homo sapiensMutation(s): 0 
Gene Names: MCOLN1ML4MSTP080
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZU1 (Homo sapiens)
Explore Q9GZU1 
Go to UniProtKB:  Q9GZU1
PHAROS:  Q9GZU1
GTEx:  ENSG00000090674 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZU1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.353α = 90
b = 94.353β = 90
c = 50.715γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM085234
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesRO1NS053494
National Basic Research Program of China (973 Program)China2014CB910301
National Natural Science Foundation of China (NSFC)China31370821
Top Talents Program of Yunnan ProvinceChina2011HA012
High-level Overseas Talents of Yunnan ProvinceChina--
China Youth 1000-Talent Program of the State Council of ChinaChina--
Beijing Advanced Innovation Center for Structural BiologyChina--

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-03-15
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.6: 2024-10-23
    Changes: Structure summary