Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	High throughput cryo-EM provides structural understanding for modulators of the lysosomal ion channel TRPML1.
Journal, issue, pages	Structure, Vol. 33, Issue 8, Page 1374-11385.e7, Year 2025
Publish date	Aug 7, 2025
Authors	Judith Reeks / Pravin Mahajan / Mellissa Clark / Suzanna R Cowan / Elena Di Daniel / Christopher P Earl / Samantha Fisher / Rhian S Holvey / Scott M Jackson / Emyr Lloyd-Evans / Carmine M Morgillo / Paul N Mortenson / Marc O'Reilly / Caroline J Richardson / Patrick Schöpf / Daniel M Tams / Helen Waller-Evans / Simon E Ward / Stuart Whibley / Pamela A Williams / Christopher N Johnson /
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 ...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.
External links	Structure / PubMed:40532704
Methods	EM (single particle)
Resolution	2.1 - 2.4 Å
Structure data	52210 9hj6 EMDB-52210, PDB-9hj6: TRPML1 in complex with compound 2 Method: EM (single particle) / Resolution: 2.3 Å 52211 9hj8 EMDB-52211, PDB-9hj8: TRPML1 in complex with compound 5 Method: EM (single particle) / Resolution: 2.1 Å 52242 9hl3 EMDB-52242, PDB-9hl3: TRPML1 in complex with compound 1a Method: EM (single particle) / Resolution: 2.1 Å 52243 9hl4 EMDB-52243, PDB-9hl4: TRPML1 in complex with compound 3 Method: EM (single particle) / Resolution: 2.1 Å 52245 9hl6 EMDB-52245, PDB-9hl6: TRPML1 in complex with compound 4a Method: EM (single particle) / Resolution: 2.2 Å 52246 9hl8 EMDB-52246, PDB-9hl8: TRPML1 in complex with compound 8 Method: EM (single particle) / Resolution: 2.2 Å 52248 9hla EMDB-52248, PDB-9hla: TRPML1 in complex with compound 9a Method: EM (single particle) / Resolution: 2.4 Å 52249 9hlb EMDB-52249, PDB-9hlb: TRPML1 in complex with compound 10 Method: EM (single particle) / Resolution: 2.1 Å 52250 9hlc EMDB-52250, PDB-9hlc: TRPML1 in complex with compound 11 Method: EM (single particle) / Resolution: 2.1 Å 52251 9hld EMDB-52251, PDB-9hld: TRPML1 in complex with compound 13 Method: EM (single particle) / Resolution: 2.2 Å
Chemicals	ChemComp-EUJ: (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 PDB-1ivc: STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE ChemComp-HEX: HEXANE ChemComp-R16: HEXADECANE ChemComp-OCT: N-OCTANE ChemComp-HOH: WATER PDB-1ivd: STRUCTURES OF AROMATIC INHIBITORS OF INFLUENZA VIRUS NEURAMINIDASE ChemComp-PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipidYM ChemComp-D10: DECANE ChemComp-D12: DODECANE PDB-1ivz: Solution structure of the SEA domain from murine hypothetical protein homologous to human mucin 16 PDB-1iv0: Solution structure of the YqgF-family protein (N-terminal fragment) ChemComp-LNK: PENTANE PDB-1iv1: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase PDB-1iv2: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form CDP) ChemComp-PLC: DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipidYM PDB-1iv3: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form MG atoms) ChemComp-8K6: Octadecane PDB-1iv4: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate) PDB-1iv5: New Crystal Form of Human CD81 Large Extracellular Loop. PDB-1iv6: Solution Structure of the DNA Complex of Human TRF1
Source	homo sapiens (human)
Keywords	MEMBRANE PROTEIN / Ion channel