5TJC

I-II linker of TRPML1 channel at pH 7.5

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • 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; National Institutes of Health/National Institute of Neurological Disorders and Stroke; National Basic Research Program; National Natural Science Foundation of China; 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: 2.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nsmb.3362
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The activities of organellar ion channels are often regulated by Ca <sup>2+ </sup> and H <sup>+ </sup>, which are present in high concentrations in many organelles. Here we report a structural element critical for dual Ca <sup>2+ </sup>/pH regulation ...

    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.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province; and Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Pharmacology, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mucolipin-1
A
223Homo sapiensMutation(s): 0 
Gene Names: MCOLN1 (ML4)
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
Endolysosomal TRPML1 channel luminal domain, pH 6
Find proteins for Q9GZU1 (Homo sapiens)
Go to Gene View: MCOLN1
Go to UniProtKB:  Q9GZU1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 182.811α = 90.00
b = 182.811β = 90.00
c = 182.811γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM085234
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesRO1NS053494
National Basic Research ProgramChina2014CB910301
National Natural Science Foundation of ChinaChina31370821
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 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-08
    Type: Database references
  • Version 1.2: 2017-03-15
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence