8Y58: TRIM21 PRYSPRY

Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine. Determined by X-ray diffraction at 1.6 Å resolution. Released 9 Oct 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,610
Mol. weight: 22.06 kDa
Ligands: PMZ
Released: 9 Oct 2024

Explore 8Y58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y58 contains 4 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: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	1
β-strand	8	1	2
α-helix	10-12	3
β-strand	17-19	3	1
β-strand	25-28	4	1
β-strand	48-49	2	3
β-strand	50	1	2
β-strand	54	1	3
β-strand	58-64	7	1
β-strand	71-77	7	3
β-strand	94-100	7	3
β-strand	104-107	4	3
β-strand	113-115	3	3
β-strand	123-129	7	1
β-strand	134-139	6	1
α-helix	140-142	3
β-strand	145-150	6	1
β-strand	159-164	6	3
α-helix	175-176	2
β-strand	177-179	3	1
α-helix	180-181	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM21	A	protein	192	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8Y58_1 E3 ubiquitin-protein ligase TRIM21 (chains A)
GPMVHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHY
WEVDVTGKEAWALGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVP
PCQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLC
PLNIGSQGSTDY

Ligands and cofactors

ID	Name	Formula	Copies
PMZ	1-[10-(3-dimethylamino-propyl)-10H-phenothiazin-2-yl]-ethanone	C19 H22 N2 O S	1

Water and common crystallization additives (FMT) are not listed.

Primary citation

Selective degradation of multimeric proteins by TRIM21-based molecular glue and PROTAC degraders. Lu, P., Cheng, Y., Xue, L. et al. Cell (2024) 187:7126-7142.e20. DOI 10.1016/j.cell.2024.10.015 · 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
9II5 1.49 Å, Crystal structure of human TRIM21 PRYSPRY in complex with compound 1
32QM 1.5 Å, Human TRIM21 PRYSPRY domain in complex with compound 5 (Z31)
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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