5IBK: Skp1-F-box

Skp1-F-box in complex with a ubiquitin variant. Determined by X-ray diffraction at 2.5 Å resolution. Released 30 Mar 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 4,284
Mol. weight: 66.61 kDa
Released: 30 Mar 2016

Explore 5IBK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IBK contains 36 α-helices and 20 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.

Chain A: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	13-17	5	1
α-helix	18-21	4
α-helix	25-32	8
β-strand	45-47	3	1
α-helix	52-64	13
α-helix	85-86	2
α-helix	87-92	6
α-helix	97-109	13
α-helix	113-127	15
α-helix	132-139	8
α-helix	141-143	3
α-helix	147-154	8

Chains B and E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	280-283	4
α-helix	286-293	8
α-helix	298-304	7
α-helix	309-319	11

Chains C and F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	4
β-strand	12-17	6	4
β-strand	22	1	5
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	4
β-strand	48-49	2	4
α-helix	50-51	2
β-strand	55	1	5
α-helix	57-59	3
β-strand	66-71	6	4

Chain D: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	6
β-strand	13-17	5	6
α-helix	18-21	4
α-helix	25-32	8
β-strand	45-47	3	6
α-helix	52-64	13
α-helix	84-86	3
α-helix	87-92	6
α-helix	97-109	13
α-helix	113-127	15
α-helix	132-139	8
α-helix	141-143	3
α-helix	147-159	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1,S-phase kinase-associated protein 1	A, D	protein	151	Homo sapiens	P63208 (AlphaFold model)
F-box/WD repeat-containing protein 7	B, E	protein	63	Homo sapiens	Q969H0 (AlphaFold model)
Polyubiquitin-B	C, F	protein	78	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5IBK_1 S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 (chains A, D)
GAMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTH
HKDDPGGSGTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTP
EEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 2 (B, E), FASTA

>5IBK_2 F-box/WD repeat-containing protein 7 (chains B, E)
GATQVKHMMQVIEPQFQRDFISLLPKELALYVLSFLEPKDLLQAAQTCRYWRILAEDNLL
WRE

Sequence of entity 3 (C, F), FASTA

>5IBK_3 Polyubiquitin-B (chains C, F)
GSGSMQIFVKTGARTAITLEVEPSDTIENVKAKIQDKEGIPPDQQILIFSRKLLEDGRTL
SDYNIHRESTLRLVLIFR

Primary citation

Inhibition of SCF ubiquitin ligases by engineered ubiquitin variants that target the Cul1 binding site on the Skp1-F-box interface. Gorelik, M., Orlicky, S., Sartori, M.A. et al. Proc Natl Acad Sci U S A (2016) 113:3527-3532. DOI 10.1073/pnas.1519389113 · 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
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
7T1Y 2.55 Å, Structure of the Fbw7-Skp1-MycCdegron complex

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