8BYL: S-phase kinase-associated protein 1

Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex. Determined by electron microscopy at 3.5 Å resolution. Released 28 Jun 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,378
Mol. weight: 98.37 kDa
Released: 28 Jun 2023

Explore 8BYL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BYL contains 29 α-helices and 22 β-strands across 3 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, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1008-1009	2	1
β-strand	1013-1014	2	1
α-helix	1025-1031	7
α-helix	1046-1056	11
α-helix	1070-1073	4
α-helix	1075-1079	5
α-helix	1090-1093	4
α-helix	1097-1110	14
α-helix	1113-1126	14
α-helix	1132-1139	8
α-helix	1149-1156	8

Chain B: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2102-2110	9
α-helix	2114-2117	4
α-helix	2119-2122	4
α-helix	2125-2131	7
β-strand	2140-2141	2	2
α-helix	2149-2157	9
β-strand	2162-2164	3	2
β-strand	2185-2187	3	2
α-helix	2195-2202	8
β-strand	2210-2212	3	2
β-strand	2217	1	3
α-helix	2220-2225	6
α-helix	2226-2228	3
β-strand	2234-2236	3	2
β-strand	2241	1	3
α-helix	2245-2254	10
β-strand	2260-2262	3	2
α-helix	2271-2280	10
β-strand	2287-2288	2	2
α-helix	2294-2296	3
α-helix	2299-2308	10
β-strand	2314-2315	2	2
β-strand	2317-2318	2	4
α-helix	2325-2327	3
α-helix	2328-2333	6
β-strand	2339	1	2
β-strand	2342-2343	2	4
α-helix	2353-2356	4
β-strand	2364	1	2
α-helix	2375-2381	7
β-strand	2416-2417	2	2
α-helix	2419-2421	3

Chain C: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3007-3008	2	5
α-helix	3009-3011	3
β-strand	3012-3014	3	5
β-strand	3017-3023	7	5
α-helix	3026-3029	4
α-helix	3040-3043	4
β-strand	3055-3059	5	5
β-strand	3066-3072	7	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-phase kinase-associated protein 1	A	protein	163	Homo sapiens	P63208 (AlphaFold model)
S-phase kinase-associated protein 2	B	protein	424	Homo sapiens	Q13309 (AlphaFold model)
Cyclin-dependent kinases regulatory subunit 1	C	protein	79	Homo sapiens	P61024 (AlphaFold model)
Cyclin-dependent kinase inhibitor 1B	D	protein	198	Homo sapiens	P46527 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8BYL_1 S-phase kinase-associated protein 1 (chains A)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Sequence of entity 2 (B), FASTA

>8BYL_2 S-phase kinase-associated protein 2 (chains B)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL

Sequence of entity 3 (C), FASTA

>8BYL_3 Cyclin-dependent kinases regulatory subunit 1 (chains C)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK

Sequence of entity 4 (D), FASTA

>8BYL_4 Cyclin-dependent kinase inhibitor 1B (chains D)
MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW
NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG
APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPN
AGSVEQTPKKPGLRRRQT

Primary citation

Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2-cyclin A-p27KIP1. Rowland, R.J., Heath, R., Maskell, D. et al. Sci Rep (2023) 13:10718-10718. DOI 10.1038/s41598-023-37609-9 · 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

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