8BYA: SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex
Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex. Determined by electron microscopy at 3.38 Å resolution. Released 28 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 3.38 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 8,389
- Mol. weight
- 177.59 kDa
- Released
- 28 Jun 2023
Explore 8BYA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8BYA contains 53 α-helices and 40 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: 11 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-20 | 3 | 1 |
| β-strand | 30-32 | 3 | 1 |
| β-strand | 35-36 | 2 | 2 |
| α-helix | 46-52 | 7 | |
| β-strand | 63 | 1 | 3 |
| β-strand | 66-68 | 3 | 1 |
| β-strand | 71 | 1 | 2 |
| β-strand | 75-76 | 2 | 2 |
| β-strand | 79-81 | 3 | 1 |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 101-104 | 4 | |
| α-helix | 109-119 | 11 | |
| α-helix | 130-132 | 3 | |
| β-strand | 134-135 | 2 | 4 |
| β-strand | 141 | 1 | 4 |
| β-strand | 143 | 1 | 3 |
| β-strand | 157 | 1 | 5 |
| α-helix | 166-168 | 3 | |
| α-helix | 171-174 | 4 | |
| β-strand | 179 | 1 | 5 |
| α-helix | 184-188 | 5 | |
| α-helix | 194-197 | 4 | |
| α-helix | 208-219 | 12 | |
| α-helix | 230-232 | 3 | |
| α-helix | 258-261 | 4 | |
Chain B: 17 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 179-192 | 14 | |
| α-helix | 194-196 | 3 | |
| α-helix | 198-201 | 4 | |
| α-helix | 208-225 | 18 | |
| α-helix | 229-243 | 15 | |
| α-helix | 253-268 | 16 | |
| α-helix | 272-274 | 3 | |
| α-helix | 275-280 | 6 | |
| α-helix | 288-301 | 14 | |
| α-helix | 311-317 | 7 | |
| α-helix | 330-342 | 13 | |
| α-helix | 352-367 | 16 | |
| α-helix | 374-380 | 7 | |
| α-helix | 388-399 | 12 | |
| α-helix | 409-413 | 5 | |
| α-helix | 416-418 | 3 | |
| α-helix | 425-426 | 2 | |
Chain C: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 38-51 | 14 | |
| α-helix | 56-60 | 5 | |
| β-strand | 62-63 | 2 | 6 |
| β-strand | 68-69 | 2 | 6 |
| β-strand | 77-79 | 3 | 1 |
Chain D: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1025-1030 | 6 | |
| α-helix | 1046-1062 | 17 | |
| α-helix | 1087-1091 | 5 | |
| α-helix | 1097-1110 | 14 | |
| α-helix | 1114-1127 | 14 | |
| α-helix | 1132-1138 | 7 | |
| α-helix | 1149-1156 | 8 | |
| α-helix | 1157-1159 | 3 | |
Chain E: 13 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2102-2110 | 9 | |
| α-helix | 2114-2118 | 5 | |
| α-helix | 2126-2131 | 6 | |
| β-strand | 2139-2141 | 3 | 7 |
| β-strand | 2146 | 1 | 8 |
| α-helix | 2152-2157 | 6 | |
| β-strand | 2162-2164 | 3 | 7 |
| β-strand | 2169 | 1 | 8 |
| β-strand | 2185-2187 | 3 | 7 |
| α-helix | 2195-2202 | 8 | |
| β-strand | 2210-2212 | 3 | 7 |
| β-strand | 2217 | 1 | 9 |
| α-helix | 2220-2225 | 6 | |
| β-strand | 2234-2236 | 3 | 7 |
| β-strand | 2241 | 1 | 9 |
| α-helix | 2245-2254 | 10 | |
| β-strand | 2260-2261 | 2 | 7 |
| α-helix | 2271-2279 | 9 | |
| β-strand | 2287-2288 | 2 | 7 |
| α-helix | 2299-2308 | 10 | |
| β-strand | 2314-2315 | 2 | 7 |
| α-helix | 2328-2331 | 4 | |
| α-helix | 2351-2358 | 8 | |
| β-strand | 2364-2365 | 2 | 10 |
| α-helix | 2372 | 1 | |
| α-helix | 2375-2382 | 8 | |
| β-strand | 2387-2388 | 2 | 10 |
| β-strand | 2408-2409 | 2 | 11 |
| β-strand | 2412-2413 | 2 | 11 |
| β-strand | 2416-2417 | 2 | 7 |
Chain F: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3007-3008 | 2 | 12 |
| β-strand | 3014 | 1 | 13 |
| β-strand | 3017 | 1 | 13 |
| β-strand | 3018-3023 | 6 | 12 |
| α-helix | 3043-3046 | 4 | |
| β-strand | 3055-3059 | 5 | 12 |
| β-strand | 3066-3071 | 6 | 12 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cyclin-dependent kinase 2 | A | protein | 298 | Homo sapiens | P24941 (AlphaFold model) |
| Cyclin-A2 | B | protein | 432 | Homo sapiens | P20248 (AlphaFold model) |
| Cyclin-dependent kinase inhibitor 1B | C | protein | 158 | Homo sapiens | P46527 (AlphaFold model) |
| S-phase kinase-associated protein 1 | D | protein | 163 | Homo sapiens | P63208 (AlphaFold model) |
| S-phase kinase-associated protein 2 | E | protein | 424 | Homo sapiens | Q13309 |
| Cyclin-dependent kinases regulatory subunit 1 | F | protein | 79 | Homo sapiens | P61024 |
| p27 KIP1 C-terminus | G | protein | 10 | Homo sapiens | P46527 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>8BYA_1 Cyclin-dependent kinase 2 (chains A)
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTTTHEVVTLWYRAPEILLGCKYY
STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Sequence of entity 2 (B), FASTA
>8BYA_2 Cyclin-A2 (chains B)
MLGNSAPGPATREAGSALLALQQTALQEDQENINPEKAAPVQQPRTRAALAVLKSGNPRG
LAQQQRPKTRRVAPLKDLPVNDEHVTVPPWKANSKQPAFTIHVDEAEKEAQKKPAESQKI
EREDALAFNSAISLPGPRKPLVPLDYPMDGSFESPHTMDMSIILEDEKPVSVNEVPDYHE
DIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYID
RFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLK
VLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAF
HLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHG
VSLLNPPETLNL
Sequence of entity 3 (C), FASTA
>8BYA_3 Cyclin-dependent kinase inhibitor 1B (chains C)
MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW
NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDGSGSRPAAPLIG
APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATD
Sequence of entity 4 (D), FASTA
>8BYA_4 S-phase kinase-associated protein 1 (chains D)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 5 (E), FASTA
>8BYA_5 S-phase kinase-associated protein 2 (chains E)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL
Sequence of entity 6 (F), FASTA
>8BYA_6 Cyclin-dependent kinases regulatory subunit 1 (chains F)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK
Sequence of entity 7 (G), FASTA
>8BYA_7 p27 KIP1 C-terminus (chains G)
AGSVEQTPKK
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 P24941 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6Q4G 0.98 Å, CDK2 in complex with FragLite37
- 6Q49 1.0 Å, CDK2 in complex with FragLite6
- 6Q4H 1.0 Å, CDK2 in complex with FragLite36
- 6Q48 1.03 Å, CDK2 in complex with FragLite7
- 6Q4J 1.05 Å, CDK2 in complex with FragLite34
- 6Q4E 1.06 Å, CDK2 in complex with FragLite33
- 6Q4K 1.06 Å, CDK2 in complex with FragLite38
- 6Q4D 1.07 Å, CDK2 in complex with FragLite31
- 6Q3B 1.11 Å, CDK2 in complex with FragLite2
- 6Q4I 1.11 Å, CDK2 in complex with FragLite35
- 6Q4B 1.12 Å, CDK2 in complex with FragLite13
- 6Q4A 1.13 Å, CDK2 in complex with FragLite14
Browse structure collections
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