7B5L: Cullin-1
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1. Determined by electron microscopy at 3.8 Å resolution. Released 10 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 21,529
- Mol. weight
- 382.22 kDa
- Ligands
- ZN, SY8
- Released
- 10 Feb 2021
Explore 7B5L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7B5L contains 124 α-helices and 94 β-strands across 12 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: 36 helices, 14 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 | 174-187 | 14 | |
| 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 | 257-274 | 18 | |
| α-helix | 284-295 | 12 | |
| α-helix | 300-312 | 13 | |
| α-helix | 318-328 | 11 | |
| α-helix | 333-353 | 21 | |
| α-helix | 356-361 | 6 | |
| α-helix | 363-383 | 21 | |
| α-helix | 389-404 | 16 | |
| α-helix | 407-411 | 5 | |
| α-helix | 418-430 | 13 | |
| α-helix | 439-455 | 17 | |
| α-helix | 461-475 | 15 | |
| α-helix | 482-496 | 15 | |
| α-helix | 502-524 | 23 | |
| α-helix | 525-527 | 3 | |
| β-strand | 534-540 | 7 | 1 |
| α-helix | 560-573 | 14 | |
| β-strand | 578-581 | 4 | 1 |
| α-helix | 583-585 | 3 | |
| β-strand | 587 | 1 | 2 |
| β-strand | 588-589 | 2 | 1 |
| β-strand | 590 | 1 | 3 |
| β-strand | 601-602 | 2 | 3 |
| β-strand | 604 | 1 | 2 |
| α-helix | 605-613 | 9 | |
| β-strand | 619-621 | 3 | 4 |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
| β-strand | 649-650 | 2 | 4 |
| β-strand | 668-671 | 4 | 4 |
| β-strand | 682-683 | 2 | 3 |
| α-helix | 706-721 | 16 | |
| β-strand | 725-726 | 2 | 5 |
| α-helix | 727-738 | 12 | |
| α-helix | 746-758 | 13 | |
| β-strand | 762-764 | 3 | 5 |
| α-helix | 765 | 1 | |
| β-strand | 771-774 | 4 | 5 |
Chain D: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-17 | 16 | |
| β-strand | 22-27 | 6 | 25 |
| β-strand | 34-39 | 6 | 25 |
| β-strand | 50 | 1 | 26 |
| β-strand | 51-56 | 6 | 25 |
| α-helix | 65-66 | 2 | |
| β-strand | 67-69 | 3 | 25 |
| β-strand | 84 | 1 | 25 |
| α-helix | 101-113 | 13 | |
| α-helix | 123-131 | 9 | |
| α-helix | 133-145 | 13 | |
| β-strand | 149 | 1 | 26 |
Chain H: 17 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 101-104 | 4 | 6 |
| α-helix | 106-124 | 19 | |
| α-helix | 128-137 | 10 | |
| α-helix | 142-150 | 9 | |
| α-helix | 155-159 | 5 | |
| β-strand | 185 | 1 | 7 |
| β-strand | 192 | 1 | 7 |
| α-helix | 195-197 | 3 | |
| β-strand | 198-199 | 2 | 8 |
| β-strand | 207-208 | 2 | 8 |
| α-helix | 209-222 | 14 | |
| β-strand | 230 | 1 | 9 |
| α-helix | 238 | 1 | |
| β-strand | 239 | 1 | 9 |
| α-helix | 240 | 1 | |
| α-helix | 242-248 | 7 | |
| α-helix | 253-269 | 17 | |
| β-strand | 275 | 1 | 6 |
| β-strand | 284-287 | 4 | 6 |
| β-strand | 294-296 | 3 | 10 |
| β-strand | 302-304 | 3 | 10 |
| β-strand | 310 | 1 | 10 |
| α-helix | 317-325 | 9 | |
| α-helix | 333-340 | 8 | |
| β-strand | 342-343 | 2 | 11 |
| β-strand | 350-351 | 2 | 11 |
| β-strand | 359-361 | 3 | 12 |
| β-strand | 370-372 | 3 | 12 |
| β-strand | 378 | 1 | 12 |
| α-helix | 409-429 | 21 | |
| α-helix | 431-447 | 17 | |
| α-helix | 453-480 | 28 | |
| α-helix | 486-512 | 27 | |
| α-helix | 518-549 | 32 | |
Chain K: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 17 |
| β-strand | 12-13 | 2 | 17 |
| β-strand | 17-23 | 7 | 17 |
| α-helix | 26-29 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 55-59 | 5 | 17 |
| β-strand | 66-72 | 7 | 17 |
Chain L: 14 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 31-36 | 6 | 27 |
| α-helix | 46-55 | 10 | |
| β-strand | 63 | 1 | 28 |
| α-helix | 64-65 | 2 | |
| β-strand | 66-71 | 6 | 27 |
| β-strand | 75-80 | 6 | 27 |
| α-helix | 81-82 | 2 | |
| β-strand | 85-86 | 2 | 28 |
| α-helix | 88-93 | 6 | |
| α-helix | 101-120 | 20 | |
| β-strand | 123-124 | 2 | 29 |
| β-strand | 133-135 | 3 | 28 |
| β-strand | 141-143 | 3 | 28 |
| α-helix | 146-148 | 3 | |
| β-strand | 150-151 | 2 | 29 |
| α-helix | 166-168 | 3 | |
| α-helix | 171-174 | 4 | |
| α-helix | 184-198 | 15 | |
| α-helix | 208-219 | 12 | |
| β-strand | 245 | 1 | 30 |
| α-helix | 248-251 | 4 | |
| α-helix | 257-264 | 8 | |
| α-helix | 277-281 | 5 | |
| α-helix | 284-287 | 4 | |
Chain N: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 20 |
| β-strand | 12-16 | 5 | 20 |
| β-strand | 22 | 1 | 21 |
| α-helix | 23-34 | 12 | |
| β-strand | 41-45 | 5 | 22 |
| β-strand | 48-49 | 2 | 22 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 21 |
| β-strand | 66 | 1 | 20 |
| β-strand | 68-71 | 4 | 22 |
Chain P: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| α-helix | 54-60 | 7 | |
| β-strand | 62-63 | 2 | 31 |
| β-strand | 68-69 | 2 | 31 |
| α-helix | 86-89 | 4 | |
Chain R: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-34 | 9 | 1 |
| β-strand | 70-73 | 4 | 23 |
| β-strand | 78-80 | 3 | 23 |
| α-helix | 81-90 | 10 | |
| β-strand | 94 | 1 | 24 |
| β-strand | 99 | 1 | 24 |
| β-strand | 103-105 | 3 | 23 |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
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 | 73 | 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 |
| NEDD8 | N | protein | 76 | Homo sapiens | Q15843 |
| E3 ubiquitin-protein ligase RBX1 | R | protein | 108 | Homo sapiens | P62877 |
| Ubiquitin-conjugating enzyme E2 L3 | D | protein | 154 | Homo sapiens | P68036 |
| 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
>7B5L_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (H), FASTA
>7B5L_2 E3 ubiquitin-protein ligase ARIH1 (chains H)
MDSDEGYNYEFDEDEECSEEDSGAEEEEDEDDDEPDDDTLDLGEVELVEPGLGVGGERDG
LLCGETGGGGGSALGPGGGGGGGGGGGGGGPGHEQEEDYRYEVLTAEQILQHMVECIREV
NEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHVINPSKKSRTRQMNTRSS
AQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILV
DDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCG
RQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSNWIAANTKECPKCHVTIEKDGGCNHM
VCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQERSRAALQRYLFYCNR
YMNHMQSLRFEHKLYAQVKQKMEEMQQHNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAF
YLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLL
QHVHEGYEKDLWEYIED
Sequence of entity 3 (T), FASTA
>7B5L_3 S-phase kinase-associated protein 2 (chains T)
MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLG
HPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKV
SGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHFSP
FRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLSGC
SGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQKS
DLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGEIP
TLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTLQK
PSCL
Sequence of entity 4 (K), FASTA
>7B5L_4 Cyclin-dependent kinases regulatory subunit 1 (chains K)
MSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIH
EPEPHILLFRRPL
Sequence of entity 5 (S), FASTA
>7B5L_5 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 6 (U), FASTA
>7B5L_6 Polyubiquitin-C (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
Sequence of entity 7 (N), FASTA
>7B5L_7 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG
Sequence of entity 8 (R), FASTA
>7B5L_8 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 9 (D), FASTA
>7B5L_9 Ubiquitin-conjugating enzyme E2 L3 (chains D)
MAASRRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAE
YPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHP
LRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD
Sequence of entity 10 (L), FASTA
>7B5L_10 Cyclin-dependent kinase 2 (chains L)
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY
STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Sequence of entity 11 (Y), FASTA
>7B5L_11 Cyclin-A2 (chains Y)
MLGNSAPGPATREAGSALLALQQTALQEDQENINPEKAAPVQQPRTRAALAVLKSGNPRG
LAQQQRPKTRRVAPLKDLPVNDEHVTVPPWKANSKQPAFTIHVDEAEKEAQKKPAESQKI
EREDALAFNSAISLPGPRKPLVPLDYPMDGSFESPHTMDMSIILEDEKPVSVNEVPDYHE
DIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYID
RFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLK
VLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAF
HLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHG
VSLLNPPETLNL
Sequence of entity 12 (P), FASTA
>7B5L_12 Cyclin-dependent kinase inhibitor 1B (chains P)
MSNVRVSNGSPSLERMDARQAEHPKPSACRNLFGPVDHEELTRDLEKHCRDMEEASQRKW
NFDFQNHKPLEGKYEWQEVEKGSLPEFYYRPPRPPKGACKVPAQESQDVSGSRPAAPLIG
APANSEDTHLVDPKTDPSDSQTGLAEQCAGIRKRPATDDSSTQNKRANRTEENVSDGSPN
AGSVEQTPKKPGLRRRQT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 9 |
| SY8 | 5-azanylpentan-2-one | C5 H11 N O | 1 |
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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