6AYF

TRPML3/ML-SA1 complex at pH 7.4

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni

  • 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; National Institutes of Health/National Institute of General Medical Sciences; 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 14 Advanced Innovation Center for Structural Biology; Tsinghua-Peking Joint Center for Life Sciences 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/nsmb.3502
  • Primary Citation of Related Structures:  

  • 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-el ...

    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

    Department of Biological Sciences, Columbia University, New York, New York, USA.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Department of Orthopedic Oncology, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mucolipin-3
A, B, C, D
558Homo sapiensMutation(s): 0 
Gene Names: MCOLN3
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
TRPML3 ion channel, apo protein at pH 7.4
Find proteins for Q8TDD5 (Homo sapiens)
Go to Gene View: MCOLN3
Go to UniProtKB:  Q8TDD5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of ChinaChina2014CB910301
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM085234
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 14 Advanced Innovation Center for Structural BiologyChina--
Tsinghua-Peking Joint Center for Life SciencesChina--
National Natural Science Foundation of ChinaChina31570730

Revision History 

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Author supporting evidence
  • Version 1.3: 2017-12-20
    Type: Database references