5WPQ

Cryo-EM structure of mammalian endolysosomal TRPML1 channel in nanodiscs in closed I conformation at 3.64 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5WPQ/pdb
• EM Map EMD-8881: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2017-08-07 Released: 2017-10-18 
• Deposition Author(s): Chen, Q., She, J., Guo, J., Bai, X., Jiang, Y.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR), Howard Hughes Medical Institute (HHMI), Cancer Prevention and Research Institute of Texas (CPRIT), Murchison Linthicum Scholar in Medical Research fund, Welch Foundation

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 268.35 kDa 
• Atom Count: 14,889 
• Modelled Residue Count: 1,816 
• Deposited Residue Count: 2,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucolipin-1	A, B, C, D	592	Mus musculus	Mutation(s): 0  Gene Names: Mcoln1 Membrane Entity: Yes
UniProt
Find proteins for Q99J21 (Mus musculus) Explore Q99J21  Go to UniProtKB:  Q99J21

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.64 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Chen, Q., She, J., Guo, J., Bai, X., Jiang, Y.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	GM079179
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	NS062792
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	AR060837
Howard Hughes Medical Institute (HHMI)	United States	--
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	--
Murchison Linthicum Scholar in Medical Research fund	United States	--
Welch Foundation	United States	I-1578

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2019-04-24
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-04-05
  Changes: Database references, Structure summary