9BIV: Ubc13 with a New Active Site Loop Conformation

Crystal Structure of Ubc13 with a New Active Site Loop Conformation. Determined by X-ray diffraction at 1.68 Å resolution. Released 8 May 2024.

Method: X-ray diffraction
Resolution: 1.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,735
Mol. weight: 33.54 kDa
Released: 8 May 2024

Explore 9BIV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BIV contains 18 α-helices and 17 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
α-helix	11-24	14
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	100-102	3
α-helix	104-107	4
α-helix	115-125	11
α-helix	129-132	4
α-helix	135-138	4
β-strand	142	1	2

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-28	6	4
β-strand	31-40	10	4
α-helix	41-42	2
β-strand	51-57	7	4
α-helix	66-67	2
β-strand	68-71	4	4
β-strand	77	1	5
β-strand	80	1	5
β-strand	85	1	4
β-strand	86	1	5
α-helix	89-91	3
α-helix	101-113	13
α-helix	122	1
α-helix	124-131	8
α-helix	133-147	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 variant 2	A	protein	145	Homo sapiens	Q15819 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B	protein	152	Homo sapiens	P61088 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9BIV_1 Ubiquitin-conjugating enzyme E2 variant 2 (chains A)
MAVSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTNYEN
RIYSLKVECGPKYPEAPPSVRFVTKINMNGINNSSGMVDARSIPVLAKWQNSYSIKVVLQ
ELRRLMMSKENMKLPQPPEGQTYNN

Sequence of entity 2 (B), FASTA

>9BIV_2 Ubiquitin-conjugating enzyme E2 N (chains B)
MAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPE
EYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDP
LANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Primary citation

Crystal Structure of Ubc13 with a New Active Site Loop Conformation. Farraj, R.A., Edwards, R.A., Glover, J.N.M. To be published.

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
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…
4NRI 2.3 Å, Crystal Structure of a human Mms2/Ubc13 A122G mutant

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