6AYG

Human Apo-TRPML3 channel at pH 4.8

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc

  • Deposited: 2017-09-08 Released: 2017-11-08 
  • Deposition Author(s): Zhou, X., Li, M., Su, D., Jia, Q., Li, H., Li, X., Yang, J.
  • Funding Organization(s): National Basic Research Program of China (973 Program), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), 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, Tsinghua-Peking Joint Center for Life Sciences

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states.

Zhou, X.Li, M.Su, D.Jia, Q.Li, H.Li, X.Yang, J.

(2017) Nat Struct Mol Biol 24: 1146-1154

  • DOI: https://doi.org/10.1038/nsmb.3502
  • Primary Citation of Related Structures:  
    6AYE, 6AYF, 6AYG

  • PubMed Abstract: 

    TRPML3 channels are mainly localized to endolysosomes and play a critical role in the endocytic pathway. Their dysfunction causes deafness and pigmentation defects in mice. TRPML3 activity is inhibited by low endolysosomal pH. Here we present cryo-electron microscopy (cryo-EM) structures of human TRPML3 in the closed, agonist-activated, and low-pH-inhibited states, with resolutions of 4.06, 3.62, and 4.65 Å, respectively. The agonist ML-SA1 lodges between S5 and S6 and opens an S6 gate. A polycystin-mucolipin domain (PMD) forms a luminal cap. S1 extends into this cap, forming a 'gating rod' that connects directly to a luminal pore loop, which undergoes dramatic conformational changes in response to low pH. S2 extends intracellularly and interacts with several intracellular regions to form a 'gating knob'. These unique structural features, combined with the results of electrophysiological studies, indicate a new mechanism by which luminal pH and other physiological modulators such as PIP 2 regulate TRPML3 by changing S1 and S2 conformations.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mucolipin-3
A, B, C, D
558Homo sapiensMutation(s): 0 
Gene Names: MCOLN3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDD5 (Homo sapiens)
Explore Q8TDD5 
Go to UniProtKB:  Q8TDD5
PHAROS:  Q8TDD5
GTEx:  ENSG00000055732 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDD5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2014CB910301
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM085234
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--
Tsinghua-Peking Joint Center for Life SciencesChina--
National Natural Science Foundation of China (NSFC)China31570730

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Author supporting evidence
  • Version 1.3: 2017-12-20
    Changes: Database references
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references