7BBD: Monoubiquitinated TRIM21 RING

Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2. Determined by X-ray diffraction at 2.2 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,434
Mol. weight: 61.2 kDa
Ligands: ZN
Released: 27 Jan 2021

Explore 7BBD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BBD contains 24 α-helices and 39 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	11-23	13
β-strand	31-35	5	9
β-strand	45-51	7	9
α-helix	52-53	2
β-strand	62-68	7	9
α-helix	77-78	2
β-strand	79-82	4	9
β-strand	84	1	10
β-strand	91	1	11
β-strand	98	1	11
α-helix	104-107	4
α-helix	115-125	11
α-helix	129-132	4
α-helix	137-138	2
β-strand	142	1	10

Chain B: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	1
β-strand	12-17	6	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
β-strand	55	1	2
β-strand	66-71	6	1
α-helix	80-89	10
β-strand	91	1	3
β-strand	98	1	3
β-strand	102-104	3	4
β-strand	110-112	3	4
α-helix	113-119	7
β-strand	124-126	3	5
β-strand	133-135	3	5
α-helix	136-138	3
β-strand	140-141	2	4
α-helix	143-156	14

Chain C: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	12
β-strand	31-40	10	12
α-helix	41-42	2
β-strand	51-57	7	12
α-helix	66-67	2
β-strand	68-71	4	12
β-strand	77	1	13
β-strand	80	1	13
β-strand	85	1	12
β-strand	86	1	13
β-strand	88	1	8
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	6
β-strand	12-16	5	6
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	6
β-strand	48-49	2	6
β-strand	55	1	7
β-strand	65-71	7	6
β-strand	75	1	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21	B	protein	164	Homo sapiens	P0CG47 (AlphaFold model), P19474 (AlphaFold model)
Polyubiquitin-C	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 variant 2	A	protein	150	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	C	protein	153	Homo sapiens	P61088

Sequence of entity 1 (B), FASTA

>7BBD_1 Polyubiquitin-B,E3 ubiquitin-protein ligase TRIM21 (chains B)
GSHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRAAMASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECIS
QVGKGGGSVCPVCRQRFLLKNLRPNRQLANMVNNLKEISQEARE

Sequence of entity 2 (D), FASTA

>7BBD_2 Polyubiquitin-C (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 3 (A), FASTA

>7BBD_3 Ubiquitin-conjugating enzyme E2 variant 2 (chains A)
GSQEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPR
TNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSI
KVVLQELRRLMMSKENMKLPQPPEGQTYNN

Sequence of entity 4 (C), FASTA

>7BBD_4 Ubiquitin-conjugating enzyme E2 N (chains C)
GMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLP
EEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILADKWSPALQIRTVLLSIQALLSAPNPDD
PLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination. Kiss, L., Clift, D., Renner, N. et al. Nat Commun (2021) 12:1220-1220. DOI 10.1038/s41467-021-21443-6 · PubMed

Other PDB entries of the same protein (UniProt P0CG47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NVG 1.07 Å, Thr12 Phosphorylated Ubiquitin
5TOG 1.08 Å, Room temperature structure of ubiquitin variant u7ub25.2540
5TOF 1.12 Å, Room temperature structure of ubiquitin variant u7ub25
4XOF 1.15 Å, Observing the overall rocking motion of a protein in a crystal - Orthorhombic Ubiquitin…
5GOD 1.15 Å, Lys27-linked di-ubiquitin
5GOB 1.15 Å, Lys6-linked di-ubiquitin
5W46 1.18 Å, Structure of S65D Phosphomimetic Ubiquitin Refined at 1.2 Angstroms Resolution
7S6O 1.25 Å, The crystal structure of Lys48-linked di-ubiquitin
8IC9 1.25 Å, Lys48-linked K48C-diubiquitin
5DK8 1.32 Å, Human ubiquitin in the P1 space group
7CAP 1.33 Å, Cyclic Lys48-linked triubiquitin
5V1Y 1.42 Å, Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin complex

Browse structure collections

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