9I0T: TRIM25 PRYSPRY covalently

Crystal structure of TRIM25 PRYSPRY covalently bound to 2-chloro-1-[4-(3-methyl-4-phenyl-phenyl)carbonyl-1,4-diazepan-1-yl]ethanone. Determined by X-ray diffraction at 1.8 Å resolution. Released 21 May 2025.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,692
Mol. weight: 23.03 kDa
Ligands: A1IZK
Released: 21 May 2025

Explore 9I0T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I0T contains 6 α-helices and 17 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	0-11	12
α-helix	15-18	4
α-helix	19-21	3
β-strand	22	1	1
β-strand	27	1	2
α-helix	29-31	3
β-strand	36-39	4	1
β-strand	44-47	4	1
α-helix	54-56	3
β-strand	66-68	3	3
β-strand	69	1	2
β-strand	73	1	3
β-strand	77-84	8	1
β-strand	90-96	7	3
α-helix	104-106	3
β-strand	114-120	7	3
β-strand	123-128	6	3
β-strand	131-135	5	3
β-strand	142-148	7	1
β-strand	153-159	7	1
β-strand	163-170	8	1
β-strand	177-183	7	3
β-strand	189-192	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin/ISG15 ligase TRIM25	A	protein	199	Homo sapiens	Q14258 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9I0T_1 E3 ubiquitin/ISG15 ligase TRIM25 (chains A)
GMASLKAKVLETFLAKSRPELLEYYIKVILDYNTAHNKVALSECYTVASVAEMPQNYRPH
PQRFTYCSQVLGLHCYKKGIHYWEVELQKNNFCGVGICYGSMNRQGPESRLGRNSASWCV
EWFNTKISAWHNNVEKTLPSTKATRVGVLLNCDHGFVIFFAVADKVHLMYKFRVDFTEAL
YPAFWVFSAGATLSICSPK

Ligands and cofactors

ID	Name	Formula	Copies
A1IZK	1-[4-(3-methyl-4-phenyl-phenyl)carbonyl-1,4-diazepan-1-yl]ethanone	C21 H24 N2 O2	1

Primary citation

Discovery and optimisation of a covalent ligand for TRIM25 and its application to targeted protein ubiquitination. McPhie, K.A., Esposito, D., Pettinger, J. et al. Chem Sci (2025) 16:10432-10443. DOI 10.1039/d5sc01540e · PubMed

Other PDB entries of the same protein (UniProt Q14258 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6FLM 2.01 Å, Crystal structure of the human TRIM25 PRYSPRY domain
5FER 2.34 Å, Complex of TRIM25 RING with UbcH5-Ub
5EYA 2.4 Å, TRIM25 RING domain in complex with Ubc13-Ub conjugate
4LTB 2.59 Å, Coiled-coil domain of TRIM25
9IUN 2.7 Å, Crystal structure of Trim25 Pspry
4CFG 2.8 Å, Structure of the TRIM25 coiled-coil
5NT1 2.82 Å, Complex of influenza A NS1 effector domain with TRIM25 coiled coil
6FLN 3.6 Å, Crystal structure of the human TRIM25 coiled-coil and PRYSPRY domains
5NT2 4.26 Å, Complex of influenza A NS1 with TRIM25 coiled coil domain

Browse structure collections

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