8R5B: Human TRIM7 PRYSPRY domain

Crystal structure of human TRIM7 PRYSPRY domain bound to (3-phenoxybenzoyl)-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: 2
Atoms: 3,101
Mol. weight: 40.3 kDa
Ligands: Y32
Released: 17 Jan 2024

Explore 8R5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R5B contains 2 α-helices and 32 β-strands across 2 chains. 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: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	346	1	1
β-strand	355-357	3	2
β-strand	363-366	4	2
β-strand	385-387	3	3
β-strand	388	1	1
β-strand	392	1	3
β-strand	396-403	8	2
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	451-452	2	3
β-strand	460-466	7	2
β-strand	471-476	6	2
β-strand	482-487	6	2
β-strand	494-500	7	3
β-strand	507-510	4	2

Chain B: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	346	1	4
β-strand	355-357	3	5
β-strand	363-366	4	5
β-strand	385-387	3	6
β-strand	388	1	4
β-strand	392	1	6
β-strand	396-403	8	5
β-strand	409-415	7	6
α-helix	428-430	3
β-strand	432-437	6	6
β-strand	442-444	3	6
β-strand	451-452	2	6
β-strand	460-466	7	5
β-strand	471-476	6	5
β-strand	481-487	7	5
β-strand	494-500	7	6
β-strand	507-510	4	5

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>8R5B_1 E3 ubiquitin-protein ligase TRIM7 (chains A, B)
GKEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGR
HHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCG
HLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP

Ligands and cofactors

ID	Name	Formula	Copies
Y32	(2~{S})-5-azanyl-5-oxidanylidene-2-[(3-phenoxyphenyl)carbonylamino]pentanoic…	C18 H18 N2 O5	2

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

Primary citation

Crystal structure of human TRIM7 PRYSPRY domain bound to (3-phenoxybenzoyl)-L-glutamine. Munoz Sosa, C.J., Kraemer, A., Knapp, S. et al. To be published.

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
8R5C 1.6 Å, Crystal structure of human TRIM7 PRYSPRY domain bound to…
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

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