7Z8V: Cullin-1
CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked. Determined by electron microscopy at 2.7 Å resolution. Released 19 Apr 2023.
- Method
- Electron microscopy
- Resolution
- 2.7 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 18,313
- Mol. weight
- 304.29 kDa
- Ligands
- ZN
- Released
- 19 Apr 2023
Explore 7Z8V in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7Z8V contains 142 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: 39 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-31 | 11 | |
| β-strand | 37 | 1 | 1 |
| α-helix | 39-53 | 15 | |
| α-helix | 88-104 | 17 | |
| α-helix | 114-136 | 23 | |
| α-helix | 138-151 | 14 | |
| α-helix | 159-167 | 9 | |
| α-helix | 168-172 | 5 | |
| α-helix | 176-191 | 16 | |
| α-helix | 199-210 | 12 | |
| 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 | 356-361 | 6 | |
| α-helix | 363-384 | 22 | |
| α-helix | 389-404 | 16 | |
| α-helix | 407-412 | 6 | |
| α-helix | 417-430 | 14 | |
| α-helix | 442-453 | 12 | |
| α-helix | 459-476 | 18 | |
| α-helix | 482-495 | 14 | |
| α-helix | 499-526 | 28 | |
| α-helix | 529-531 | 3 | |
| β-strand | 534-541 | 8 | 2 |
| α-helix | 554-556 | 3 | |
| α-helix | 560-573 | 14 | |
| β-strand | 577-592 | 16 | 2 |
| β-strand | 599-604 | 6 | 2 |
| α-helix | 605-612 | 8 | |
| 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 | 681-683 | 3 | 2 |
| α-helix | 686-688 | 3 | |
| α-helix | 689-721 | 33 | |
| β-strand | 724-726 | 3 | 4 |
| α-helix | 727-738 | 12 | |
| α-helix | 746-758 | 13 | |
| β-strand | 762-764 | 3 | 4 |
| α-helix | 765 | 1 | |
| β-strand | 771-774 | 4 | 4 |
Chain D: 76 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-14 | 9 | |
| α-helix | 20-35 | 16 | |
| α-helix | 43-56 | 14 | |
| α-helix | 62-77 | 16 | |
| α-helix | 81-95 | 15 | |
| α-helix | 100-116 | 17 | |
| α-helix | 128-143 | 16 | |
| α-helix | 149-163 | 15 | |
| α-helix | 170-172 | 3 | |
| α-helix | 173-180 | 8 | |
| α-helix | 181-185 | 5 | |
| α-helix | 189-204 | 16 | |
| α-helix | 208-223 | 16 | |
| α-helix | 228-244 | 17 | |
| α-helix | 247-252 | 6 | |
| α-helix | 253-264 | 12 | |
| α-helix | 269-285 | 17 | |
| α-helix | 288-293 | 6 | |
| α-helix | 294-305 | 12 | |
| α-helix | 347-363 | 17 | |
| 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 | 473-484 | 12 | |
| α-helix | 491-506 | 16 | |
| α-helix | 510-516 | 7 | |
| α-helix | 517-528 | 12 | |
| α-helix | 533-550 | 18 | |
| α-helix | 562-564 | 3 | |
| α-helix | 565-576 | 12 | |
| α-helix | 583-600 | 18 | |
| α-helix | 607-618 | 12 | |
| α-helix | 626-636 | 11 | |
| α-helix | 645-657 | 13 | |
| α-helix | 664-680 | 17 | |
| α-helix | 682-684 | 3 | |
| α-helix | 687-694 | 8 | |
| α-helix | 698-700 | 3 | |
| α-helix | 706-722 | 17 | |
| α-helix | 724-730 | 7 | |
| 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 | 814-825 | 12 | |
| α-helix | 832-848 | 17 | |
| α-helix | 857-863 | 7 | |
| α-helix | 870-886 | 17 | |
| α-helix | 892-901 | 10 | |
| α-helix | 909-918 | 10 | |
| α-helix | 922-925 | 4 | |
| α-helix | 929-939 | 11 | |
| α-helix | 947-960 | 14 | |
| α-helix | 967-975 | 9 | |
| α-helix | 979-990 | 12 | |
| α-helix | 1001-1012 | 12 | |
| α-helix | 1013-1016 | 4 | |
| α-helix | 1020-1036 | 17 | |
| α-helix | 1038-1040 | 3 | |
| α-helix | 1042-1044 | 3 | |
| α-helix | 1045-1054 | 10 | |
| α-helix | 1060-1062 | 3 | |
| β-strand | 1063-1068 | 6 | 1 |
| β-strand | 1071-1076 | 6 | 1 |
| α-helix | 1079-1094 | 16 | |
| α-helix | 1102-1112 | 11 | |
| α-helix | 1117-1132 | 16 | |
| α-helix | 1135-1140 | 6 | |
| α-helix | 1142-1154 | 13 | |
| α-helix | 1163-1184 | 22 | |
| α-helix | 1193-1204 | 12 | |
| α-helix | 1206-1214 | 9 | |
Chain F: 13 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 102-109 | 8 | |
| α-helix | 114-120 | 7 | |
| α-helix | 125-130 | 6 | |
| β-strand | 139-141 | 3 | 8 |
| α-helix | 149-157 | 9 | |
| β-strand | 162-164 | 3 | 8 |
| β-strand | 169-170 | 2 | 9 |
| α-helix | 179-181 | 3 | |
| β-strand | 185-187 | 3 | 8 |
| β-strand | 192-193 | 2 | 9 |
| α-helix | 195-202 | 8 | |
| β-strand | 210-212 | 3 | 8 |
| α-helix | 220-226 | 7 | |
| β-strand | 234 | 1 | 10 |
| α-helix | 245-254 | 10 | |
| β-strand | 260-262 | 3 | 10 |
| α-helix | 271-279 | 9 | |
| β-strand | 287-289 | 3 | 10 |
| α-helix | 299-308 | 10 | |
| β-strand | 314-316 | 3 | 10 |
| α-helix | 325-333 | 9 | |
| β-strand | 339-341 | 3 | 10 |
| α-helix | 350-358 | 9 | |
| β-strand | 364-366 | 3 | 10 |
| α-helix | 375-382 | 8 | |
| β-strand | 387-388 | 2 | 10 |
Chain R: 5 helices, 8 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 | 60-61 | 2 | |
| α-helix | 63-66 | 4 | |
| β-strand | 70-73 | 4 | 6 |
| β-strand | 78-80 | 3 | 6 |
| α-helix | 81-87 | 7 | |
| β-strand | 93 | 1 | 7 |
| β-strand | 100 | 1 | 7 |
| α-helix | 101 | 1 | |
| β-strand | 103-105 | 3 | 6 |
Chain S: 9 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 11 |
| β-strand | 13-17 | 5 | 11 |
| α-helix | 18-21 | 4 | |
| α-helix | 25-28 | 4 | |
| α-helix | 44 | 1 | |
| β-strand | 45-46 | 2 | 11 |
| α-helix | 52-64 | 13 | |
| α-helix | 87-93 | 7 | |
| α-helix | 97-110 | 14 | |
| α-helix | 113-126 | 14 | |
| α-helix | 132-139 | 8 | |
| α-helix | 147-156 | 10 | |
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 2 | F | protein | 426 | Homo sapiens | Q13309 (AlphaFold model) |
| S-phase kinase-associated protein 1 | S | protein | 149 | Homo sapiens | P63208 |
Sequence of entity 1 (C), FASTA
>7Z8V_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (D), FASTA
>7Z8V_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
KTLEDPDLNVRRVALVTFNSAAHNKPSLIRDLLDTVLPHLYNETKVRKELIREVEMGPFK
HTVDDGLDIRKAAFECMYTLLDSCLDRLDIFEFLNHVEDGLKDHYDIKMLTFLMLVRLST
LCPSAVLQRLDRLVEPLRATCTTKVKANSVKQEFEKQDELKRSAMRAVAALLTIPEAEKS
PLMSEFQSQISSNPELAAIFESIQKDSSSTNLESMDTS
Sequence of entity 3 (R), FASTA
>7Z8V_3 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 4 (F), FASTA
>7Z8V_4 S-phase kinase-associated protein 2 (chains F)
GSMHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSN
LGHPESPPRKRLKSKGSDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELL
KVSGVCKRWYRLASDESLWQTLDLTGKNLHPDVTGRLLSQGVIAFRCPRSFMDQPLAEHF
SPFRVQHMDLSNSVIEVSTLHGILSQCSKLQNLSLEGLRLSDPIVNTLAKNSNLVRLNLS
GCSGFSEFALQTLLSSCSRLDELNLSWCFDFTEKHVQVAVAHVSETITQLNLSGYRKNLQ
KSDLSTLVRRCPNLVHLDLSDSVMLKNDCFQEFFQLNYLQHLSLSRCYDIIPETLLELGE
IPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLTL
QKPSCL
Sequence of entity 5 (S), FASTA
>7Z8V_5 S-phase kinase-associated protein 1 (chains S)
MPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDPVPLPNVNAAILKKVIQWCTHHK
DDPGGSGTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEE
IRKTFNIKNDFTEEEEAQVRKENQWCEEK
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
- 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…
- 9EFV 3.03 Å, Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3
Browse structure collections
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