7B5M: Cullin-1
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2. Determined by electron microscopy at 3.91 Å resolution. Released 17 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.91 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 12,530
- Mol. weight
- 273.3 kDa
- Ligands
- ZN
- Released
- 17 Feb 2021
Explore 7B5M in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7B5M contains 66 α-helices and 58 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: 33 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-31 | 11 | |
| α-helix | 39-53 | 15 | |
| α-helix | 86-105 | 20 | |
| α-helix | 115-136 | 22 | |
| α-helix | 138-139 | 2 | |
| α-helix | 140-144 | 5 | |
| α-helix | 159-171 | 13 | |
| α-helix | 175-187 | 13 | |
| α-helix | 199-210 | 12 | |
| α-helix | 227-228 | 2 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-251 | 18 | |
| α-helix | 257-275 | 19 | |
| α-helix | 284-295 | 12 | |
| α-helix | 300-312 | 13 | |
| α-helix | 318-328 | 11 | |
| α-helix | 336-355 | 20 | |
| α-helix | 356-359 | 4 | |
| α-helix | 363-381 | 19 | |
| α-helix | 391-403 | 13 | |
| α-helix | 407-411 | 5 | |
| α-helix | 417-430 | 14 | |
| α-helix | 439-454 | 16 | |
| α-helix | 459-475 | 17 | |
| α-helix | 482-500 | 19 | |
| α-helix | 502-524 | 23 | |
| α-helix | 525-527 | 3 | |
| β-strand | 534-541 | 8 | 1 |
| α-helix | 557-559 | 3 | |
| α-helix | 560-573 | 14 | |
| β-strand | 582 | 1 | 1 |
| β-strand | 587-590 | 4 | 1 |
| β-strand | 601-604 | 4 | 1 |
| α-helix | 605-612 | 8 | |
| α-helix | 613-615 | 3 | |
| β-strand | 621 | 1 | 2 |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
| β-strand | 649-650 | 2 | 3 |
| β-strand | 668 | 1 | 2 |
| β-strand | 670-671 | 2 | 3 |
| β-strand | 682-683 | 2 | 1 |
Chain H: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 317-324 | 8 | |
| α-helix | 332-340 | 9 | |
| β-strand | 353 | 1 | 4 |
| β-strand | 361 | 1 | 5 |
| β-strand | 370 | 1 | 5 |
| β-strand | 382 | 1 | 6 |
| β-strand | 384 | 1 | 6 |
| α-helix | 404-429 | 26 | |
| α-helix | 431-447 | 17 | |
| α-helix | 453-480 | 28 | |
| α-helix | 488-511 | 24 | |
| α-helix | 518-549 | 32 | |
Chain K: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 13 |
| β-strand | 18 | 1 | 14 |
| β-strand | 21 | 1 | 15 |
| β-strand | 23 | 1 | 13 |
| α-helix | 26-29 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 55-60 | 6 | 15 |
| β-strand | 63-70 | 8 | 15 |
| β-strand | 71 | 1 | 14 |
Chain R: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-33 | 8 | 1 |
| α-helix | 54-57 | 4 | |
| β-strand | 71-73 | 3 | 19 |
| β-strand | 78-79 | 2 | 19 |
| α-helix | 84-90 | 7 | |
| β-strand | 94 | 1 | 20 |
| β-strand | 97 | 1 | 20 |
| β-strand | 103-105 | 3 | 19 |
Chain S: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 16 |
| β-strand | 13-16 | 4 | 16 |
| α-helix | 25-30 | 6 | |
| β-strand | 39-40 | 2 | 16 |
| α-helix | 46-58 | 13 | |
| α-helix | 87-90 | 4 | |
| α-helix | 97-110 | 14 | |
| α-helix | 113-127 | 15 | |
| α-helix | 132-138 | 7 | |
| α-helix | 150-156 | 7 | |
Chain T: 14 helices, 22 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 | 7 |
| β-strand | 146 | 1 | 8 |
| α-helix | 149-157 | 9 | |
| β-strand | 162-164 | 3 | 7 |
| β-strand | 169 | 1 | 8 |
| α-helix | 180 | 1 | |
| β-strand | 181 | 1 | 9 |
| β-strand | 185-187 | 3 | 7 |
| α-helix | 195-202 | 8 | |
| β-strand | 205 | 1 | 9 |
| β-strand | 210-212 | 3 | 7 |
| β-strand | 217 | 1 | 10 |
| α-helix | 220-226 | 7 | |
| β-strand | 234-236 | 3 | 7 |
| β-strand | 241 | 1 | 10 |
| α-helix | 245-254 | 10 | |
| β-strand | 260-262 | 3 | 7 |
| α-helix | 271-280 | 10 | |
| β-strand | 287-289 | 3 | 7 |
| α-helix | 299-308 | 10 | |
| β-strand | 314-316 | 3 | 7 |
| α-helix | 325-333 | 9 | |
| β-strand | 339-341 | 3 | 7 |
| α-helix | 354-357 | 4 | |
| β-strand | 364-366 | 3 | 7 |
| β-strand | 368 | 1 | 11 |
| β-strand | 371 | 1 | 11 |
| α-helix | 376-382 | 7 | |
| β-strand | 387-388 | 2 | 7 |
| β-strand | 409 | 1 | 12 |
| β-strand | 412 | 1 | 12 |
| β-strand | 416 | 1 | 7 |
Chain U: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-5 | 2 | 17 |
| β-strand | 13-14 | 2 | 17 |
| α-helix | 23-34 | 12 | |
| β-strand | 41-45 | 5 | 18 |
| β-strand | 48-50 | 3 | 18 |
| β-strand | 68-71 | 4 | 18 |
| β-strand | 73 | 1 | 4 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-1 | C | protein | 776 | Homo sapiens | Q13616 (AlphaFold model) |
| E3 ubiquitin-protein ligase ARIH1 | H | protein | 557 | Homo sapiens | Q9Y4X5 (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 |
| Polyubiquitin-C | U | protein | 75 | Homo sapiens | P0CG48 |
| E3 ubiquitin-protein ligase RBX1 | R | protein | 108 | Homo sapiens | P62877 |
| Cyclin-dependent kinase inhibitor 1B | P | protein | 198 | Homo sapiens | P46527 |
Sequence of entity 1 (C), FASTA
>7B5M_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (H), FASTA
>7B5M_2 E3 ubiquitin-protein ligase ARIH1 (chains H)
MDSDEGYNYEFDEDEECSEEDSGAEEEEDEDDDEPDDDTLDLGEVELVEPGLGVGGERDG
LLCGETGGGGGSALGPGGGGGGGGGGGGGGPGHEQEEDYRYEVLTAEQILQHMVECIREV
NEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHVINPSKKSRTRQMNTRSS
AQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILV
DDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCG
RQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSNWIAANTKECPKCHVTIEKDGGCNHM
VCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQERSRAALQRYLFYCNR
YMNHMQSLRAAHKLYAQVKQKMEEMQQHNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAF
YLKKNNQSIIFENNQADLENATAVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLL
QHVHEGYEKDLWEYIED
Sequence of entity 3 (T), FASTA
>7B5M_3 S-phase kinase-associated protein 2 (chains T)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL
Sequence of entity 4 (K), FASTA
>7B5M_4 Cyclin-dependent kinases regulatory subunit 1 (chains K)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPLPKKPKK
Sequence of entity 5 (S), FASTA
>7B5M_5 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 6 (U), FASTA
>7B5M_6 Polyubiquitin-C (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
Sequence of entity 7 (R), FASTA
>7B5M_7 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 8 (P), FASTA
>7B5M_8 Cyclin-dependent kinase inhibitor 1B (chains P)
MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW
NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG
APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTSNKRANRTEENVSDGSPN
AGSVEQTPRRPGLRRRQT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 5 |
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…
Browse structure collections
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