7BBF: Ubiquitin charged Ube2N

Crystal structure of ubiquitin charged Ube2N (Ube2N~Ub) in complex with Ube2V2. Determined by X-ray diffraction at 2.54 Å resolution. Released 27 Jan 2021.

Method: X-ray diffraction
Resolution: 2.54 Å
Organism: Homo sapiens
Chains: 9
Atoms: 8,651
Mol. weight: 128.07 kDa
Released: 27 Jan 2021

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

Secondary structure: helices and β-sheets

7BBF contains 60 α-helices and 70 β-strands across 9 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: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	14
β-strand	34-40	7	14
α-helix	41-42	2
β-strand	51-57	7	14
α-helix	66-67	2
β-strand	68-71	4	14
β-strand	80	1	15
β-strand	85	1	14
β-strand	86	1	15
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain B: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-23	13
β-strand	31-35	5	4
β-strand	45-51	7	4
α-helix	52-53	2
β-strand	62-68	7	4
α-helix	77-78	2
β-strand	79-82	4	4
β-strand	84	1	5
β-strand	91	1	6
β-strand	97	1	4
β-strand	98	1	6
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	137-138	2
β-strand	142	1	5

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	18
β-strand	12-16	5	18
β-strand	22	1	19
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	18
β-strand	48-50	3	18
α-helix	51	1
β-strand	55	1	19
β-strand	66-71	6	18
α-helix	72	1

Chains D and G: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
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	80	1	13
β-strand	85	1	12
β-strand	86	1	13
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain E: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-23	13
β-strand	31-35	5	7
β-strand	45-51	7	7
α-helix	52-53	2
β-strand	62-68	7	7
α-helix	77-78	2
β-strand	79-82	4	7
β-strand	84	1	8
β-strand	88	1	9
β-strand	91	1	9
β-strand	97	1	7
β-strand	98	1	9
α-helix	99	1
α-helix	100-102	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	137-138	2
β-strand	142	1	8

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	12-16	5	20
β-strand	22	1	21
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	20
β-strand	48-49	2	20
α-helix	50-51	2
β-strand	55	1	21
β-strand	66-71	6	20
α-helix	72	1

Chain H: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-23	13
β-strand	31-35	5	1
β-strand	45-51	7	1
α-helix	52-53	2
β-strand	62-68	7	1
α-helix	77-78	2
β-strand	79-82	4	1
β-strand	84	1	2
β-strand	91	1	3
β-strand	97	1	1
β-strand	98	1	3
α-helix	104-107	4
α-helix	115-126	12
α-helix	134-138	5
β-strand	142	1	2

Chain I: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	16
β-strand	12-16	5	16
β-strand	22	1	17
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-49	2	16
α-helix	50-51	2
β-strand	55	1	17
β-strand	66-71	6	16
α-helix	72-73	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 variant 2	B, E, H	protein	150	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	A, D, G	protein	153	Homo sapiens	P61088 (AlphaFold model)
Polyubiquitin-C	C, F, I	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (B, E, H), FASTA

>7BBF_1 Ubiquitin-conjugating enzyme E2 variant 2 (chains B, E, H)
GSQEFMAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPR
TNYENRIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSI
KVVLQELRRLMMSKENMKLPQPPEGQTYNN

Sequence of entity 2 (A, D, G), FASTA

>7BBF_2 Ubiquitin-conjugating enzyme E2 N (chains A, D, G)
GMAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLP
EEYPMAAPKVRFMTKIYHPNVDKLGRIKLDILADKWSPALQIRTVLLSIQALLSAPNPDD
PLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C, F, I), FASTA

>7BBF_3 Polyubiquitin-C (chains C, F, I)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

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 Q15819 (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
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
8WR5 1.7 Å, The Crystal Structure of Mms2 from Biortus
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
1J74 1.9 Å, Crystal Structure of Mms2
4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
9N1F 2.1 Å, Crystal Structure of the Ark2C-Ubc13~Ub-Mms2 complex
7BBD 2.2 Å, Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin…

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