6BVA: Ubiquitin Variant

Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Determined by X-ray diffraction at 2.66 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 2.66 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,111
Mol. weight: 68.92 kDa
Released: 18 Jul 2018

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

Secondary structure: helices and β-sheets

6BVA contains 32 α-helices and 24 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 B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	5
β-strand	10	1	6
β-strand	11d	1	6
β-strand	12-17	6	5
β-strand	22	1	7
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	5
β-strand	48-49	2	5
α-helix	50-51	2
β-strand	55	1	7
α-helix	57-59	3
β-strand	66-71	6	5

Chain C: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	13-17	5	8
α-helix	18-21	4
α-helix	25-31	7
β-strand	45-46	2	8
α-helix	52-64	13
α-helix	68-74	7
α-helix	87-92	6
α-helix	97-110	14
α-helix	113-125	13
α-helix	132-139	8
α-helix	147-156	10

Chain D: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	13-17	5	1
α-helix	18-21	4
α-helix	25-29	5
β-strand	45-46	2	1
α-helix	52-64	13
α-helix	68-74	7
α-helix	87-92	6
α-helix	97-110	14
α-helix	113-125	13
α-helix	132-138	7
α-helix	148-156	9

Chains E and F: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1067-1074	8
α-helix	1079-1085	7
α-helix	1090-1095	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1	C, D	protein	165	Homo sapiens	P63208 (AlphaFold model)
Lysine-specific demethylase 2B	E, F	protein	47	Homo sapiens	Q8NHM5 (AlphaFold model)
Polyubiquitin-B	A, B	protein	86	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (C, D), FASTA

>6BVA_1 S-phase kinase-associated protein 1 (chains C, D)
GAMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKV
IQWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDV
TCKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 2 (E, F), FASTA

>6BVA_2 Lysine-specific demethylase 2B (chains E, F)
GAGAAHVMHREVWMAVFSYLSHQDLCVCMRVCRTWNRWCCDKRLWTR

Sequence of entity 3 (A, B), FASTA

>6BVA_3 Polyubiquitin-B (chains A, B)
GSGMQIFVKTFRDRLRNLLPQTITLEVEPSDTIENVKAKIQDKEGIPPDQQVLIFSRKRL
EDGRTLSDYNIQKESTLRLVLVFGRR

Primary citation

A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases. Gorelik, M., Manczyk, N., Pavlenco, A. et al. Structure (2018) 26:1226. DOI 10.1016/j.str.2018.06.004 · PubMed

Other PDB entries of the same protein (UniProt P63208 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FS1 1.8 Å, Insights into scf ubiquitin ligases from the structure of the SKP1-SKP2 complex
6M90 2.05 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex
2AST 2.3 Å, Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
6M92 2.35 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex
2E31 2.4 Å, Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
6M91 2.4 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex
2OVR 2.5 Å, Structure of the Skp1-Fbw7-CyclinEdegN complex
6M93 2.5 Å, Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex
6WNX 2.5 Å, FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide
5IBK 2.5 Å, Skp1-F-box in complex with a ubiquitin variant
6O60 2.5 Å, Crystal structure of GGTase3-FBXL2-SKP1 complex
5JH5 2.55 Å, Structural Basis for the Hierarchical Assembly of the Core of PRC1.1

Browse structure collections

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