6D6I: Ube2V1

Ube2V1 in complex with ubiquitin variant Ubv.V1.1 and Ube2N/Ubc13. Determined by X-ray diffraction at 2.55 Å resolution. Released 17 Jul 2019.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,118
Mol. weight: 87.08 kDa
Released: 17 Jul 2019

Explore 6D6I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D6I contains 37 α-helices and 50 β-strands across 6 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.

Chains A and D: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	13-25	13
β-strand	33-37	5	1
β-strand	47-53	7	1
β-strand	54	1	2
α-helix	55	1
β-strand	61	1	2
β-strand	64-70	7	1
α-helix	79-80	2
β-strand	81-84	4	1
β-strand	86	1	3
β-strand	93	1	4
β-strand	99	1	1
β-strand	100	1	4
α-helix	102-104	3
α-helix	106-109	4
α-helix	117-127	11
α-helix	131-134	4
α-helix	137-140	4
β-strand	144	1	3

Chains B and E: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	24-27	4	5
β-strand	35-38	4	5
β-strand	53-57	5	5
α-helix	66-67	2
β-strand	68-71	4	5
β-strand	80	1	6
β-strand	85	1	5
β-strand	86	1	6
α-helix	89-92	4
α-helix	101-113	13
α-helix	126-131	6
α-helix	133-146	14

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
β-strand	41-44	4	7
β-strand	49	1	7
α-helix	50-51	2
β-strand	55	1	8
α-helix	56-59	4
β-strand	66-71	6	7

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	15
β-strand	12-16	5	15
β-strand	22	1	16
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	15
β-strand	48-49	2	15
α-helix	50-51	2
β-strand	55	1	16
α-helix	56-59	4
β-strand	66-71	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 variant 1	A, D	protein	143	Homo sapiens	Q13404 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 N	B, E	protein	155	Homo sapiens	P61088 (AlphaFold model)
Ubv.V1.1	C, F	protein	88	Homo sapiens	Q96H31 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6D6I_1 Ubiquitin-conjugating enzyme E2 variant 1 (chains A, D)
GSTGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRI
YSLKIECGPKYPEAPPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQEL
RRLMMSKENMKLPQPPEGQCYSN

Sequence of entity 2 (B, E), FASTA

>6D6I_2 Ubiquitin-conjugating enzyme E2 N (chains B, E)
GAMGSGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELF
LPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNP
DDPLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 3 (C, F), FASTA

>6D6I_3 Ubv.V1.1 (chains C, F)
GAGGDYKDDDDKMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGK
QLEDGRTLSDYNIHWESTLLLWWRLLIA

Primary citation

Structural and Functional Analysis of Ubiquitin-based Inhibitors That Target the Backsides of E2 Enzymes. Garg, P., Ceccarelli, D.F., Keszei, A.F.A. et al. J Mol Biol (2020) 432:952-966. DOI 10.1016/j.jmb.2019.09.024 · PubMed

Other PDB entries of the same protein (UniProt Q13404 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2A4D 1.69 Å, Structure of the human ubiquitin-conjugating enzyme E2 variant 1 (UEV-1)
2C2V 2.9 Å, Crystal structure of the CHIP-UBC13-UEV1a complex
2HLW Solution Structure of the Human Ubiquitin-conjugating Enzyme Variant Uev1a

Browse structure collections

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