6S53: TRIM21 RING domain

Name: PDB 6S53: Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate
Published: 2019-09-11
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate. Determined by X-ray diffraction at 2.8 Å resolution. Released 11 Sept 2019.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 12
Atoms: 9,476
Mol. weight: 141.49 kDa
Ligands: ZN
Released: 11 Sept 2019

Explore 6S53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S53 contains 59 α-helices and 97 β-strands across 12 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-13	10
β-strand	15	1	13
β-strand	22	1	13
α-helix	23	1
β-strand	26-28	3	14
β-strand	34-36	3	14
α-helix	37-43	7
β-strand	48-50	3	15
β-strand	57-59	3	15
α-helix	60-62	3
β-strand	64-65	2	14
α-helix	67-80	14

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-13	10
β-strand	15	1	10
β-strand	22	1	10
α-helix	23	1
β-strand	26-28	3	11
β-strand	34-36	3	11
α-helix	37-43	7
β-strand	48-50	3	12
β-strand	57-59	3	12
α-helix	60-62	3
β-strand	64-65	2	11
α-helix	67-79	13

Chains C and K: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	20	1	5
β-strand	23-28	6	5
β-strand	31-40	10	5
α-helix	41-42	2
β-strand	51-57	7	5
β-strand	68-71	4	5
β-strand	77	1	6
β-strand	80	1	6
β-strand	85	1	5
β-strand	86	1	6
β-strand	88	1	7
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	8
β-strand	12-16	5	8
β-strand	22	1	9
α-helix	23-34	12
β-strand	41-45	5	8
β-strand	48-49	2	8
β-strand	55	1	9
α-helix	57-59	3
α-helix	65	1
β-strand	66-71	6	8
β-strand	75	1	7

Chain E: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
β-strand	20	1	1
β-strand	23-28	6	1
β-strand	31-40	10	1
α-helix	41-42	2
β-strand	51-57	7	1
α-helix	66-67	2
β-strand	68-71	4	1
β-strand	77	1	2
β-strand	80	1	2
β-strand	85	1	1
β-strand	86	1	2
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain F: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	3
β-strand	12-16	5	3
β-strand	22	1	4
α-helix	23-34	12
β-strand	41-45	5	3
β-strand	48-49	2	3
β-strand	55	1	4
α-helix	57-59	3
α-helix	65	1
β-strand	66-71	6	3

Chain G: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	15	1	29
β-strand	22	1	29
α-helix	23	1
β-strand	26-28	3	30
β-strand	34-36	3	30
α-helix	37-43	7
β-strand	49-50	2	31
β-strand	57-58	2	31
α-helix	60-62	3
β-strand	64-65	2	30
α-helix	67-80	14

Chain H: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
β-strand	15	1	26
β-strand	22	1	26
α-helix	23	1
β-strand	26-28	3	27
β-strand	34-36	3	27
α-helix	37-43	7
β-strand	49-50	2	28
β-strand	57-58	2	28
α-helix	60-62	3
β-strand	64-65	2	27
α-helix	67-81	15

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 N	C, E, I, K	protein	152	Homo sapiens	P61088 (AlphaFold model)
Polyubiquitin-C	D, F, J, L	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
E3 ubiquitin-protein ligase TRIM21	A, B, G, H	protein	85	Homo sapiens	P19474 (AlphaFold model)

Sequence of entity 1 (C, E, I, K), FASTA

>6S53_1 Ubiquitin-conjugating enzyme E2 N (chains C, E, I, K)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRIKLDILADKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 2 (D, F, J, L), FASTA

>6S53_2 Polyubiquitin-C (chains D, F, J, L)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (A, B, G, H), FASTA

>6S53_3 E3 ubiquitin-protein ligase TRIM21 (chains A, B, G, H)
MASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQRFLL
KNLRPNRQLANMVNNLKEISQEARE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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

Primary citation

A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases. Kiss, L., Zeng, J., Dickson, C.F. et al. Nat Commun (2019) 10:4502-4502. DOI 10.1038/s41467-019-12388-y · PubMed

Other PDB entries of the same protein (UniProt P61088 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ONL 1.35 Å, Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
4ONM 1.35 Å, Crystal structure of human Mms2/Ubc13 - NSC697923
5YWR 1.47 Å, Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
4ONN 1.5 Å, Crystal structure of human Mms2/Ubc13 - BAY 11-7082
9BIV 1.68 Å, Crystal Structure of Ubc13 with a New Active Site Loop Conformation
9LHJ 1.68 Å, UBE2N/UBE2V2 complexed with a covalent inhibitor
4DHI 1.8 Å, Structure of C. elegans OTUB1 bound to human UBC13
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
4TKP 2.08 Å, Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor

Browse structure collections

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