7B5R: Cullin-1
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27. Determined by electron microscopy at 3.8 Å resolution. Released 10 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 11,606
- Mol. weight
- 270.83 kDa
- Released
- 10 Feb 2021
Explore 7B5R in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7B5R contains 74 α-helices and 34 β-strands across 7 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 C: 17 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-31 | 13 | |
| α-helix | 39-52 | 14 | |
| α-helix | 86-105 | 20 | |
| α-helix | 115-136 | 22 | |
| α-helix | 140-143 | 4 | |
| α-helix | 159-171 | 13 | |
| α-helix | 177-187 | 11 | |
| α-helix | 188-190 | 3 | |
| α-helix | 199-210 | 12 | |
| α-helix | 226-228 | 3 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-252 | 19 | |
| α-helix | 257-277 | 21 | |
| α-helix | 284-295 | 12 | |
| α-helix | 300-312 | 13 | |
| α-helix | 317-328 | 12 | |
| α-helix | 332-339 | 8 | |
Chain K: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 5 |
| β-strand | 13 | 1 | 5 |
| β-strand | 17-23 | 7 | 5 |
| α-helix | 26-29 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 55-56 | 2 | 5 |
| β-strand | 66-72 | 7 | 5 |
Chain L: 12 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-36 | 6 | 7 |
| α-helix | 46-55 | 10 | |
| β-strand | 63 | 1 | 8 |
| β-strand | 69-71 | 3 | 7 |
| β-strand | 75-80 | 6 | 7 |
| β-strand | 85-86 | 2 | 9 |
| α-helix | 88-93 | 6 | |
| α-helix | 101-120 | 20 | |
| β-strand | 123-124 | 2 | 10 |
| α-helix | 130-132 | 3 | |
| β-strand | 134-135 | 2 | 9 |
| β-strand | 141-142 | 2 | 9 |
| β-strand | 143 | 1 | 8 |
| α-helix | 146-148 | 3 | |
| β-strand | 150-151 | 2 | 10 |
| α-helix | 171-174 | 4 | |
| α-helix | 184-198 | 15 | |
| α-helix | 208-219 | 12 | |
| α-helix | 248-251 | 4 | |
| α-helix | 257-264 | 8 | |
| α-helix | 277-280 | 4 | |
| α-helix | 284-287 | 4 | |
Chain P: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| α-helix | 55-60 | 6 | |
| β-strand | 63 | 1 | 11 |
| β-strand | 68 | 1 | 11 |
| α-helix | 86-89 | 4 | |
Chain S: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 6 |
| β-strand | 14-17 | 4 | 6 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-32 | 8 | |
| β-strand | 39-40 | 2 | 6 |
| α-helix | 46-58 | 13 | |
| α-helix | 87-92 | 6 | |
| α-helix | 97-110 | 14 | |
| α-helix | 113-127 | 15 | |
| α-helix | 132-138 | 7 | |
| α-helix | 150-155 | 6 | |
Chain T: 13 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 97-99 | 3 | |
| α-helix | 102-109 | 8 | |
| α-helix | 114-120 | 7 | |
| α-helix | 125-130 | 6 | |
| β-strand | 139-141 | 3 | 1 |
| α-helix | 149-157 | 9 | |
| β-strand | 162-164 | 3 | 1 |
| β-strand | 185 | 1 | 2 |
| β-strand | 187 | 1 | 1 |
| α-helix | 195-202 | 8 | |
| β-strand | 210 | 1 | 2 |
| α-helix | 220-226 | 7 | |
| β-strand | 234 | 1 | 3 |
| α-helix | 245-254 | 10 | |
| β-strand | 260-262 | 3 | 3 |
| α-helix | 271-280 | 10 | |
| β-strand | 287-289 | 3 | 3 |
| α-helix | 299-308 | 10 | |
| β-strand | 314-316 | 3 | 3 |
| α-helix | 325-333 | 9 | |
| β-strand | 339-341 | 3 | 3 |
| α-helix | 351-358 | 8 | |
| β-strand | 364-366 | 3 | 3 |
| α-helix | 375-382 | 8 | |
| β-strand | 388 | 1 | 3 |
| β-strand | 409 | 1 | 4 |
| β-strand | 412 | 1 | 4 |
Chain Y: 19 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 179-189 | 11 | |
| α-helix | 194-196 | 3 | |
| α-helix | 199-202 | 4 | |
| α-helix | 208-224 | 17 | |
| α-helix | 229-243 | 15 | |
| α-helix | 250-252 | 3 | |
| α-helix | 253-268 | 16 | |
| α-helix | 272-274 | 3 | |
| α-helix | 275-281 | 7 | |
| α-helix | 288-302 | 15 | |
| α-helix | 311-319 | 9 | |
| α-helix | 327-342 | 16 | |
| α-helix | 352-368 | 17 | |
| α-helix | 374-380 | 7 | |
| α-helix | 388-400 | 13 | |
| α-helix | 401-403 | 3 | |
| α-helix | 408-412 | 5 | |
| α-helix | 416-418 | 3 | |
| α-helix | 421-423 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-1 | C | protein | 776 | Homo sapiens | Q13616 (AlphaFold model) |
| S-phase kinase-associated protein 2 | T | protein | 424 | Homo sapiens | Q13309 (AlphaFold model) |
| Cyclin-dependent kinases regulatory subunit 1 | K | protein | 79 | Homo sapiens | P61024 (AlphaFold model) |
| S-phase kinase-associated protein 1 | S | protein | 163 | Homo sapiens | P63208 (AlphaFold model) |
| Cyclin-dependent kinase 2 | L | protein | 298 | Homo sapiens | P24941 |
| Cyclin-A2 | Y | protein | 432 | Homo sapiens | P20248 |
| Cyclin-dependent kinase inhibitor 1B | P | protein | 198 | Homo sapiens | P46527 |
Sequence of entity 1 (C), FASTA
>7B5R_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (T), FASTA
>7B5R_2 S-phase kinase-associated protein 2 (chains T)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL
Sequence of entity 3 (K), FASTA
>7B5R_3 Cyclin-dependent kinases regulatory subunit 1 (chains K)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK
Sequence of entity 4 (S), FASTA
>7B5R_4 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 5 (L), FASTA
>7B5R_5 Cyclin-dependent kinase 2 (chains L)
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY
STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Sequence of entity 6 (Y), FASTA
>7B5R_6 Cyclin-A2 (chains Y)
MLGNSAPGPATREAGSALLALQQTALQEDQENINPEKAAPVQQPRTRAALAVLKSGNPRG
LAQQQRPKTRRVAPLKDLPVNDEHVTVPPWKANSKQPAFTIHVDEAEKEAQKKPAESQKI
EREDALAFNSAISLPGPRKPLVPLDYPMDGSFESPHTMDMSIILEDEKPVSVNEVPDYHE
DIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYID
RFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLK
VLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAF
HLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHG
VSLLNPPETLNL
Sequence of entity 7 (P), FASTA
>7B5R_7 Cyclin-dependent kinase inhibitor 1B (chains P)
MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW
NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG
APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPN
AGSVEQTPKKPGLRRRQT
Primary citation
Ubiquitin ligation to F-box protein targets by SCF-RBR E3-E3 super-assembly. Horn-Ghetko, D., Krist, D.T., Prabu, J.R. et al. Nature (2021) 590:671-676. DOI 10.1038/s41586-021-03197-9 · PubMed
Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
- 5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
- 3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
- 8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
- 7Z8R 2.7 Å, CAND1-CUL1-RBX1
- 7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
- 8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
- 9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
- 1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
- 4F52 3.0 Å, Structure of a Glomulin-RBX1-CUL1 complex
- 7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
- 9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…
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