5TJA | pdb_00005tja

I-II linker of TRPML1 channel at pH 6

  • 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: 2.30 Å
  • R-Value Free: 
    0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.227 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5TJA

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 25.2 kDa 
  • Atom Count: 1,629 
  • Modeled Residue Count: 191 
  • Deposited Residue Count: 223 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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: 2.30 Å
  • R-Value Free:  0.253 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.227 (DCC) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.321α = 90
b = 125.321β = 90
c = 76.68γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
CNSrefinement
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: 2024-10-23
    Changes: Data collection, Database references, Structure summary