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: MCOLN1ML4TRPML1MSTP080
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