8R5C: Human TRIM7 PRYSPRY domain

Name: PDB 8R5C: Crystal structure of human TRIM7 PRYSPRY domain bound to (2-(1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine
Published: 2024-01-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of human TRIM7 PRYSPRY domain bound to (2-(1-oxoisoindolin-2-yl)-3-phenylpropanoyl)-L-glutamine. Determined by X-ray diffraction at 1.6 Å resolution. Released 17 Jan 2024.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,595
Mol. weight: 20.64 kDa
Ligands: SRT, Y3C
Released: 17 Jan 2024

Explore 8R5C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R5C contains 2 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: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	341	1	1
β-strand	346	1	2
β-strand	355-357	3	1
β-strand	363-366	4	1
β-strand	385-387	3	3
β-strand	388	1	2
β-strand	392	1	3
β-strand	396-403	8	1
β-strand	409-415	7	3
α-helix	428-430	3
β-strand	432-438	7	3
β-strand	441-444	4	3
β-strand	451-453	3	3
β-strand	460-466	7	1
β-strand	471-476	6	1
α-helix	477-479	3
β-strand	481-487	7	1
β-strand	494-500	7	3
β-strand	507-509	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM7	A	protein	175	Homo sapiens	Q9C029 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8R5C_1 E3 ubiquitin-protein ligase TRIM7 (chains A)
GKEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGR
HHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCG
HLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP

Ligands and cofactors

ID	Name	Formula	Copies
SRT	S,r meso-tartaric acid	C4 H6 O6	2
Y3C	(2~{S})-5-azanyl-5-oxidanylidene-2-[[(2~{S})-2-(3-oxidanylidene-1~{H}-isoindol-…	C22 H23 N3 O5	1

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

Primary citation

A C-Degron Structure-Based Approach for the Development of Ligands Targeting the E3 Ligase TRIM7. Munoz Sosa, C.J., Lenz, C., Hamann, A. et al. ACS Chem Biol (2024) 19:1638-1647. DOI 10.1021/acschembio.4c00301 · PubMed

Other PDB entries of the same protein (UniProt Q9C029 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7W0Q 1.1 Å, TRIM7 in complex with C-terminal peptide of 2C
7X70 1.25 Å, TRIM7 in complex with C-terminal peptide of NSP8
7X6Y 1.39 Å, TRIM7 in complex with C-terminal peptide of NSP5
7W0S 1.4 Å, TRIM7 in complex with C-terminal peptide of 2C
7X6Z 1.43 Å, TRIM7 in complex with C-terminal peptide of NSP12
9HIN 1.55 Å, Crystal structure of human TRIM7 PRYSPRY domain bound to…
7W0T 1.57 Å, TRIM7 in complex with C-terminal peptide of 2C
6UMA 1.6 Å, Crystal structure of the TRIM7 B30.2 domain at 1.6 angstrom resolution
8R5B 1.6 Å, Crystal structure of human TRIM7 PRYSPRY domain bound to (3-phenoxybenzoyl)-L-glutamine
8A5L 1.62 Å, TRIM7 PRYSPRY in complex with a 2BC peptide TIEALFQ
7OVX 1.7 Å, E3 RING ligase binding domain
7Y3A 1.7 Å, Crystal structure of TRIM7 bound to 2C

Browse structure collections

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