9II5: Human TRIM21 PRYSPRY

Crystal structure of human TRIM21 PRYSPRY in complex with compound 1. Determined by X-ray diffraction at 1.49 Å resolution. Released 7 May 2025.

Method: X-ray diffraction
Resolution: 1.49 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,549
Mol. weight: 20.64 kDa
Ligands: A1D9F
Released: 7 May 2025

Explore 9II5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9II5 contains 3 α-helices and 16 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: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	291	1	1
α-helix	293-295	3
β-strand	300-302	3	2
β-strand	308-311	4	2
α-helix	318-320	3
β-strand	331-332	2	3
β-strand	333	1	1
β-strand	337	1	3
β-strand	341-347	7	2
β-strand	354-360	7	3
β-strand	377-382	6	3
β-strand	388-390	3	3
β-strand	396-398	3	3
β-strand	406-412	7	2
β-strand	417-422	6	2
β-strand	428-433	6	2
β-strand	442-447	6	3
α-helix	458-459	2
β-strand	460-462	3	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	A	protein	178	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9II5_1 E3 ubiquitin-protein ligase TRIM21 (chains A)
VHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYWEV
DVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPPCQ
VGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTALC

Ligands and cofactors

ID	Name	Formula	Copies
A1D9F	~{N}-[(1-fluoranylcyclohexyl)methyl]-~{N}-methyl-4-(2-methylsulfanylphenyl)-2-m…	C23 H28 F N O3 S2	1

Primary citation

Chemically Induced Nuclear Pore Complex Protein Degradation via TRIM21. Li, X., Wang, Q., Guo, A. et al. ACS Chem Biol (2025) 20:1020-1028. DOI 10.1021/acschembio.4c00833 · PubMed

Other PDB entries of the same protein (UniProt P19474 (AlphaFold model), which also has an AlphaFold model), best resolution first:

32QO 1.3 Å, Human TRIM21 PRYSPRY domain in complex with compound 28 (Z38)
9PLM 1.32 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-021)
32QL 1.4 Å, Human TRIM21 PRYSPRY domain in complex with HGC652
9QBA 1.45 Å, Human TRIM21 PRYSPRY domain in complex with AL236
32QM 1.5 Å, Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
8Y58 1.6 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine.
9PLL 1.6 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-056)
8Y5B 1.74 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine.
32QN 1.8 Å, Human TRIM21 PRYSPRY domain in complex with compound 29 (Z37)
8Y59 1.89 Å, Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine.
5OLM 1.95 Å, TRIM21
9M3N 2.08 Å, Crystal structure of human TRIM21 PRYSPRY in complex with T-02

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