8A58: TRIM21 RING E3 ligase

Name: PDB 8A58: X-ray structure of TRIM21 RING E3 ligase in complex with E2 enzyme Ube2W
Published: 2023-04-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

X-ray structure of TRIM21 RING E3 ligase in complex with E2 enzyme Ube2W. Determined by X-ray diffraction at 2.25 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,513
Mol. weight: 54.51 kDa
Ligands: ZN
Released: 26 Apr 2023

Explore 8A58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A58 contains 22 α-helices and 30 β-strands across 4 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
α-helix	19-20	2
β-strand	23-26	4	1
β-strand	36-42	7	1
α-helix	43-44	2
β-strand	53-59	7	1
α-helix	68-69	2
β-strand	70-74	5	1
β-strand	81	1	2
β-strand	84	1	2
β-strand	89	1	1
β-strand	90	1	2
α-helix	93-95	3
α-helix	105-116	12
α-helix	128-135	8

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-17	18
α-helix	19-20	2
β-strand	23-25	3	9
β-strand	36-42	7	9
α-helix	43-44	2
β-strand	53-59	7	9
α-helix	68-69	2
β-strand	70-74	5	9
β-strand	81	1	10
β-strand	84	1	10
β-strand	89	1	9
β-strand	90	1	10
α-helix	93-95	3
α-helix	105-118	14
α-helix	128-135	8

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-13	9
β-strand	15	1	3
β-strand	22	1	3
β-strand	26-28	3	4
β-strand	34-36	3	4
α-helix	37-43	7
β-strand	48-50	3	5
β-strand	57-59	3	5
α-helix	60-62	3
β-strand	64-65	2	4
α-helix	67-80	14

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
β-strand	15	1	6
β-strand	22	1	6
β-strand	26-28	3	7
β-strand	34-36	3	7
α-helix	37-43	7
β-strand	48-50	3	8
β-strand	57-59	3	8
α-helix	60-62	3
β-strand	64-65	2	7
α-helix	67-80	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 W	A, B	protein	153	Homo sapiens	Q96B02 (AlphaFold model)
E3 ubiquitin-protein ligase TRIM21	C, D	protein	85	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8A58_1 Ubiquitin-conjugating enzyme E2 W (chains A, B)
SHMASMQKRLQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLF
KFSSRYPFKSPQVMFTGENIPVHPHVYSNGHIKLSILTEDWSPALSVQSVCLSIISMLSS
CKEKRRPPDNSFYVRTCNKNPKKTKWWYHDDTC

Sequence of entity 2 (C, D), FASTA

>8A58_2 E3 ubiquitin-protein ligase TRIM21 (chains C, D)
MASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQRFLL
KNLRPNRQLANMVNNLKEISQEARE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates. Kiss, L., Rhinesmith, T., Luptak, J. et al. Nat Commun (2023) 14:2160-2160. DOI 10.1038/s41467-023-37504-x · PubMed

Other PDB entries of the same protein (UniProt Q96B02 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A7L 1.82 Å, Structure of the human hypothetical ubiquitin-conjugating enzyme, LOC55284
2MT6 Solution structure of the human ubiquitin conjugating enzyme Ube2w

Browse structure collections

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