8CDK: Cullin-1
CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked. Determined by electron microscopy at 3.32 Å resolution. Released 19 Apr 2023.
- Method
- Electron microscopy
- Resolution
- 3.32 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 16,905
- Mol. weight
- 306.2 kDa
- Ligands
- ZN
- Released
- 19 Apr 2023
Explore 8CDK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8CDK contains 145 α-helices and 37 β-strands across 5 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: 40 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-32 | 16 | |
| α-helix | 39-54 | 16 | |
| α-helix | 86-105 | 20 | |
| α-helix | 113-136 | 24 | |
| α-helix | 138-139 | 2 | |
| α-helix | 140-145 | 6 | |
| α-helix | 146-150 | 5 | |
| α-helix | 159-167 | 9 | |
| α-helix | 168-172 | 5 | |
| α-helix | 173-192 | 20 | |
| α-helix | 198-211 | 14 | |
| α-helix | 226-228 | 3 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-254 | 21 | |
| α-helix | 257-278 | 22 | |
| α-helix | 281-283 | 3 | |
| α-helix | 284-296 | 13 | |
| α-helix | 297-299 | 3 | |
| α-helix | 300-312 | 13 | |
| α-helix | 316-326 | 11 | |
| α-helix | 334-353 | 20 | |
| α-helix | 358-360 | 3 | |
| α-helix | 363-384 | 22 | |
| α-helix | 389-404 | 16 | |
| α-helix | 407-412 | 6 | |
| α-helix | 417-430 | 14 | |
| β-strand | 431 | 1 | 1 |
| α-helix | 442-453 | 12 | |
| α-helix | 459-476 | 18 | |
| β-strand | 479 | 1 | 1 |
| α-helix | 482-495 | 14 | |
| α-helix | 499-525 | 27 | |
| α-helix | 530-531 | 2 | |
| β-strand | 534-541 | 8 | 2 |
| α-helix | 549-552 | 4 | |
| α-helix | 557-559 | 3 | |
| α-helix | 560-573 | 14 | |
| β-strand | 577-592 | 16 | 2 |
| β-strand | 600-604 | 5 | 2 |
| α-helix | 605-609 | 5 | |
| β-strand | 619-621 | 3 | 3 |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
| β-strand | 649-650 | 2 | 3 |
| β-strand | 668-671 | 4 | 3 |
| β-strand | 682-683 | 2 | 2 |
| α-helix | 691-721 | 31 | |
| β-strand | 724-726 | 3 | 4 |
| α-helix | 727-738 | 12 | |
| α-helix | 746-758 | 13 | |
| β-strand | 762-764 | 3 | 4 |
| β-strand | 771-774 | 4 | 4 |
Chain D: 74 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 20-35 | 16 | |
| α-helix | 43-56 | 14 | |
| α-helix | 62-78 | 17 | |
| α-helix | 81-95 | 15 | |
| α-helix | 100-115 | 16 | |
| α-helix | 128-142 | 15 | |
| α-helix | 148-163 | 16 | |
| α-helix | 173-183 | 11 | |
| α-helix | 189-204 | 16 | |
| α-helix | 208-223 | 16 | |
| α-helix | 228-245 | 18 | |
| α-helix | 246-252 | 7 | |
| α-helix | 253-263 | 11 | |
| α-helix | 269-285 | 17 | |
| α-helix | 291-293 | 3 | |
| α-helix | 294-305 | 12 | |
| α-helix | 347-361 | 15 | |
| α-helix | 365-367 | 3 | |
| α-helix | 368-370 | 3 | |
| α-helix | 371-375 | 5 | |
| α-helix | 376-381 | 6 | |
| α-helix | 382-384 | 3 | |
| α-helix | 388-405 | 18 | |
| α-helix | 424-442 | 19 | |
| α-helix | 448-464 | 17 | |
| α-helix | 470-472 | 3 | |
| α-helix | 473-484 | 12 | |
| α-helix | 491-506 | 16 | |
| α-helix | 517-528 | 12 | |
| α-helix | 533-550 | 18 | |
| α-helix | 562-576 | 15 | |
| α-helix | 583-600 | 18 | |
| α-helix | 607-620 | 14 | |
| α-helix | 626-636 | 11 | |
| α-helix | 645-657 | 13 | |
| α-helix | 658-660 | 3 | |
| α-helix | 664-680 | 17 | |
| α-helix | 687-696 | 10 | |
| α-helix | 698-700 | 3 | |
| α-helix | 706-722 | 17 | |
| α-helix | 724-729 | 6 | |
| α-helix | 733-742 | 10 | |
| α-helix | 750-765 | 16 | |
| α-helix | 772-785 | 14 | |
| α-helix | 789-790 | 2 | |
| α-helix | 794-809 | 16 | |
| α-helix | 811-813 | 3 | |
| α-helix | 814-826 | 13 | |
| α-helix | 832-846 | 15 | |
| α-helix | 857-863 | 7 | |
| α-helix | 870-886 | 17 | |
| α-helix | 888-901 | 14 | |
| α-helix | 907-919 | 13 | |
| α-helix | 922-925 | 4 | |
| α-helix | 926-928 | 3 | |
| α-helix | 929-938 | 10 | |
| α-helix | 947-960 | 14 | |
| α-helix | 963-975 | 13 | |
| α-helix | 979-989 | 11 | |
| α-helix | 990-992 | 3 | |
| α-helix | 1001-1012 | 12 | |
| α-helix | 1020-1036 | 17 | |
| α-helix | 1038-1040 | 3 | |
| α-helix | 1045-1056 | 12 | |
| α-helix | 1060-1062 | 3 | |
| α-helix | 1079-1095 | 17 | |
| α-helix | 1102-1113 | 12 | |
| α-helix | 1117-1132 | 16 | |
| α-helix | 1135-1138 | 4 | |
| α-helix | 1142-1153 | 12 | |
| α-helix | 1163-1184 | 22 | |
| α-helix | 1193-1204 | 12 | |
| α-helix | 1206-1215 | 10 | |
Chain F: 17 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 102-108 | 7 | |
| α-helix | 109-111 | 3 | |
| α-helix | 114-121 | 8 | |
| α-helix | 125-131 | 7 | |
| α-helix | 136-138 | 3 | |
| β-strand | 139-141 | 3 | 10 |
| α-helix | 149-157 | 9 | |
| β-strand | 162-164 | 3 | 10 |
| β-strand | 169 | 1 | 11 |
| α-helix | 179-181 | 3 | |
| β-strand | 185-187 | 3 | 10 |
| β-strand | 192 | 1 | 11 |
| α-helix | 195-202 | 8 | |
| β-strand | 210 | 1 | 10 |
| α-helix | 220-226 | 7 | |
| β-strand | 234 | 1 | 12 |
| α-helix | 245-254 | 10 | |
| β-strand | 260-262 | 3 | 12 |
| α-helix | 271-279 | 9 | |
| β-strand | 287-289 | 3 | 12 |
| α-helix | 299-308 | 10 | |
| β-strand | 314-316 | 3 | 12 |
| α-helix | 325-333 | 9 | |
| β-strand | 339-341 | 3 | 12 |
| α-helix | 350-358 | 9 | |
| β-strand | 364-366 | 3 | 12 |
| α-helix | 372 | 1 | |
| α-helix | 375-382 | 8 | |
| β-strand | 387-388 | 2 | 12 |
| α-helix | 412-414 | 3 | |
Chain R: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-35 | 14 | 2 |
| β-strand | 41 | 1 | 5 |
| β-strand | 48 | 1 | 5 |
| α-helix | 54-58 | 5 | |
| α-helix | 60 | 1 | |
| α-helix | 63-66 | 4 | |
| β-strand | 70-71 | 2 | 6 |
| β-strand | 72-73 | 2 | 7 |
| β-strand | 79-80 | 2 | 6 |
| α-helix | 81-87 | 7 | |
| β-strand | 93 | 1 | 8 |
| β-strand | 100 | 1 | 8 |
| α-helix | 101 | 1 | |
| β-strand | 103-105 | 3 | 7 |
Chain S: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 9 |
| β-strand | 14-16 | 3 | 9 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-33 | 9 | |
| α-helix | 44 | 1 | |
| β-strand | 45-46 | 2 | 9 |
| α-helix | 52-64 | 13 | |
| α-helix | 87-93 | 7 | |
| α-helix | 97-109 | 13 | |
| α-helix | 113-127 | 15 | |
| α-helix | 132-139 | 8 | |
| α-helix | 147-158 | 12 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-1 | C | protein | 776 | Homo sapiens | Q13616 (AlphaFold model) |
| Cullin-associated NEDD8-dissociated protein 1 | D | protein | 1238 | Homo sapiens | Q86VP6 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1, N-terminally processed | R | protein | 106 | Homo sapiens | P62877 (AlphaFold model) |
| S-phase kinase-associated protein 1 | S | protein | 163 | Homo sapiens | P63208 (AlphaFold model) |
| S-phase kinase-associated protein 2 | F | protein | 426 | Homo sapiens | Q13309 |
Sequence of entity 1 (C), FASTA
>8CDK_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (D), FASTA
>8CDK_2 Cullin-associated NEDD8-dissociated protein 1 (chains D)
GSPEFPGRMASASYHISNLLEKMTSSDKDFRFMATNDLMTELQKDSIKLDDDSERKVVKM
ILKLLEDKNGEVQNLAVKCLGPLVSKVKEYQVETIVDTLCTNMLSDKEQLRDISSIGLKT
VIGELPPASSGSALAANVCKKITGRLTSAIAKQEDVSVQLEALDIMADMLSRQGGLLVNF
HPSILTCLLPQLTSPRLAVRKRTIIALGHLVMSCGNIVFVDLIEHLLSELSKNDSMSTTR
TYIQCIAAISRQAGHRIGEYLEKIIPLVVKFCNVDDDELREYCIQAFESFVRRCPKEVYP
HVSTIINICLKYLTYDPNYNYDDEDEDENAMDADGGDDDDQGSDDEYSDDDDMSWKVRRA
AAKCLDAVVSTRHEMLPEFYKTVSPALISRFKEREENVKADVFHAYLSLLKQTRPVQSWL
CDPDAMEQGETPLTMLQSQVPNIVKALHKQMKEKSVKTRQCCFNMLTELVNVLPGALTQH
IPVLVPGIIFSLNDKSSSSNLKIDALSCLYVILCNHSPQVFHPHVQALVPPVVACVGDPF
YKITSEALLVTQQLVKVIRPLDQPSSFDATPYIKDLFTCTIKRLKAADIDQEVKERAISC
MGQIICNLGDNLGSDLPNTLQIFLERLKNEITRLTTVKALTLIAGSPLKIDLRPVLGEGV
PILASFLRKNQRALKLGTLSALDILIKNYSDSLTAAMIDAVLDELPPLISESDMHVSQMA
ISFLTTLAKVYPSSLSKISGSILNELIGLVRSPLLQGGALSAMLDFFQALVVTGTNNLGY
MDLLRMLTGPVYSQSTALTHKQSYYSIAKCVAALTRACPKEGPAVVGQFIQDVKNSRSTD
SIRLLALLSLGEVGHHIDLSGQLELKSVILEAFSSPSEEVKSAASYALGSISVGNLPEYL
PFVLQEITSQPKRQYLLLHSLKEIISSASVVGLKPYVENIWALLLKHCECAEEGTRNVVV
ECLGKLTLIDPETLLPRLKGYLISGSSYARSSVVTAVKFTISDHPQPIDPLLKNCIGDFL
KTLEDPDLNVRRVALVTFNSAAHNKPSLIRDLLDTVLPHLYNETKVRKELIREVEWGQFK
HTVDDGLDIRKAAFECMYTLLDSCLDRLDIFEFLNHVEDGLKDHYDIKMLTFLMLVRLST
LCPSAVLQRLDRLVEPLRATCTTKVKANSVKQEFEKQDELKRSAMRAVAALLTIPEAEKS
PLMSEFQSQISSNPELAAIFESIQKDSSSTNLESMDTS
Sequence of entity 3 (R), FASTA
>8CDK_3 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 4 (S), FASTA
>8CDK_4 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQ
WCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTC
KTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 5 (F), FASTA
>8CDK_5 S-phase kinase-associated protein 2 (chains F)
GSMHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSN
LGHPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELL
KVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHF
SPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLS
GCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQ
KSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGE
IPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTL
QKPSCL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
Primary citation
Systemwide disassembly and assembly of SCF ubiquitin ligase complexes. Baek, K., Scott, D.C., Henneberg, L.T. et al. Cell (2023) 186:1895. DOI 10.1016/j.cell.2023.02.035 · 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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