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 9HL6 | pdb_00009hl6

TRPML1 in complex with compound 4a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9HL6

This is version 1.1 of the entry. See complete history. 

Literature

High throughput cryo-EM provides structural understanding for modulators of the lysosomal ion channel TRPML1.

Reeks, J., Mahajan, P., Clark, M., Cowan, S.R., Di Daniel, E., Earl, C.P., Fisher, S., Holvey, R.S., Jackson, S.M., Lloyd-Evans, E., Morgillo, C.M., Mortenson, P.N., O'Reilly, M., Richardson, C.J., Schopf, P., Tams, D.M., Waller-Evans, H., Ward, S.E., Whibley, S., Williams, P.A., Johnson, C.N.

(2025) Structure 33: 1374-1385.e7

  • DOI: https://doi.org/10.1016/j.str.2025.05.014
  • Primary Citation Related Structures: 
    9HJ6, 9HJ8, 9HL3, 9HL4, 9HL6, 9HL8, 9HLA, 9HLB, 9HLC, 9HLD

  • PubMed Abstract: 

    Access to high-resolution structural data for protein-ligand complexes is a prerequisite for structure-based medicinal chemistry, where the ability to iterate cycles of design-structure-redesign is highly desirable. For proteins refractory to X-ray crystallography, such as integral membrane proteins, enablement of high throughput structure determination by cryoelectron microscopy (cryo-EM) has the potential to be transformational for structure-based design. We have applied such an approach to the lysosomal ion channel transient receptor potential mucolipin 1 (TRPML1) in complex with ten chemically diverse modulators, both agonists and antagonists. The resulting depth of high-resolution structural data generated provides important insights into protein-ligand structure-function relationships, including mechanistic understanding of ligand-induced channel pore opening and closing. Moreover, the knowledge gained has the potential to support iterative design cycles toward improved modulators of this important biological target.


  • Organizational Affiliation: 
    • Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK.

Macromolecule Content 

  • Total Structure Weight: 291.58 kDa 
  • Atom Count: 15,760 
  • Modeled Residue Count: 1,828 
  • Deposited Residue Count: 2,512 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mucolipin-1A,
B [auth C],
C [auth B],
D
628Homo sapiensMutation(s): 0 
Gene Names: MCOLN1, ML4, TRPML1, MSTP080
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9GZU1-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EUJ

Query on EUJ



Download:Ideal Coordinates CCD File
CA [auth B],
IA [auth D],
N [auth A],
U [auth C]
(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate
C25 H49 O19 P3
QXHVLVSULWMTCV-DICZBTHZSA-N
A1IV1
(Subject of Investigation/LOI)

Query on A1IV1



Download:Ideal Coordinates CCD File
DA [auth B],
JA [auth D],
O [auth A],
V [auth C]
4-[[(3R)-3-[1-(4-chloranyl-2-fluoranyl-phenyl)piperidin-4-yl]-3-methyl-2H-indol-1-yl]sulfonyl]-N,N-dimethyl-benzenesulfonamide
C28 H31 Cl F N3 O4 S2
JFSNLYLCRUYJAP-MUUNZHRXSA-N
R16

Query on R16



Download:Ideal Coordinates CCD File
L [auth A],
P [auth A],
W [auth C],
X [auth B]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
AA [auth B]
FA [auth D]
GA [auth D]
J [auth A]
K [auth A]
AA [auth B],
FA [auth D],
GA [auth D],
J [auth A],
K [auth A],
R [auth C],
S [auth C],
Z [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX

Query on HEX



Download:Ideal Coordinates CCD File
BA [auth B],
HA [auth D],
M [auth A],
T [auth C]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
LNK

Query on LNK



Download:Ideal Coordinates CCD File
EA [auth D],
I [auth A],
Q [auth C],
Y [auth B]
PENTANE
C5 H12
OFBQJSOFQDEBGM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4
MODEL REFINEMENTPHENIX1.21rc1-5101

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references