8UBU: Cullin-1
Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation. Determined by electron microscopy at 4.6 Å resolution. Released 6 Nov 2024.
- Method
- Electron microscopy
- Resolution
- 4.6 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 19,760
- Mol. weight
- 352.54 kDa
- Released
- 6 Nov 2024
Explore 8UBU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8UBU contains 124 α-helices and 66 β-strands across 10 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 A: 33 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-32 | 15 | |
| α-helix | 44-53 | 10 | |
| α-helix | 86-103 | 18 | |
| α-helix | 115-136 | 22 | |
| α-helix | 138-139 | 2 | |
| α-helix | 140-145 | 6 | |
| α-helix | 146-149 | 4 | |
| α-helix | 159-171 | 13 | |
| α-helix | 178-187 | 10 | |
| α-helix | 198-210 | 13 | |
| α-helix | 227-228 | 2 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-254 | 21 | |
| α-helix | 260-277 | 18 | |
| α-helix | 284-295 | 12 | |
| α-helix | 300-312 | 13 | |
| α-helix | 316-328 | 13 | |
| α-helix | 334-355 | 22 | |
| α-helix | 363-384 | 22 | |
| α-helix | 389-404 | 16 | |
| α-helix | 407-412 | 6 | |
| α-helix | 417-429 | 13 | |
| α-helix | 439-453 | 15 | |
| α-helix | 459-475 | 17 | |
| α-helix | 482-495 | 14 | |
| α-helix | 499-526 | 28 | |
| β-strand | 534-536 | 3 | 1 |
| β-strand | 539-541 | 3 | 2 |
| α-helix | 554-556 | 3 | |
| α-helix | 560-573 | 14 | |
| β-strand | 577-581 | 5 | 2 |
| α-helix | 583-585 | 3 | |
| β-strand | 587 | 1 | 1 |
| β-strand | 589-591 | 3 | 3 |
| β-strand | 600-602 | 3 | 3 |
| α-helix | 605-612 | 8 | |
| α-helix | 613-615 | 3 | |
| α-helix | 622-629 | 8 | |
| α-helix | 633-644 | 12 | |
Chains B and I: 0 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-28 | 3 | 1 |
| β-strand | 31-35 | 5 | 2 |
Chains C and G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 4 |
| β-strand | 13-17 | 5 | 4 |
| α-helix | 28-33 | 6 | |
| β-strand | 46 | 1 | 4 |
| α-helix | 54-64 | 11 | |
| α-helix | 87-92 | 6 | |
| α-helix | 103-109 | 7 | |
| α-helix | 113-124 | 12 | |
| α-helix | 131-138 | 8 | |
| α-helix | 150-156 | 7 | |
Chains D and K: 17 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 326-333 | 8 | |
| α-helix | 338-343 | 6 | |
| α-helix | 350-355 | 6 | |
| α-helix | 371-373 | 3 | |
| α-helix | 378-381 | 4 | |
| β-strand | 392 | 1 | 5 |
| α-helix | 401-410 | 10 | |
| β-strand | 416 | 1 | 6 |
| β-strand | 418 | 1 | 5 |
| β-strand | 419 | 1 | 7 |
| α-helix | 427-435 | 9 | |
| β-strand | 442 | 1 | 6 |
| β-strand | 445 | 1 | 7 |
| α-helix | 454-462 | 9 | |
| β-strand | 468 | 1 | 8 |
| β-strand | 471 | 1 | 7 |
| α-helix | 480-487 | 8 | |
| β-strand | 494 | 1 | 8 |
| β-strand | 497 | 1 | 9 |
| β-strand | 520-522 | 3 | 8 |
| β-strand | 523 | 1 | 9 |
| β-strand | 529 | 1 | 10 |
| α-helix | 530-533 | 4 | |
| α-helix | 534-537 | 4 | |
| β-strand | 544-546 | 3 | 8 |
| β-strand | 551 | 1 | 10 |
| α-helix | 555-564 | 10 | |
| β-strand | 570 | 1 | 8 |
| α-helix | 582-590 | 9 | |
| β-strand | 598-599 | 2 | 11 |
| α-helix | 608-614 | 7 | |
| β-strand | 623-624 | 2 | 11 |
| α-helix | 632-641 | 10 | |
| α-helix | 660-667 | 8 | |
| α-helix | 681-689 | 9 | |
Chain E: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-28 | 11 | |
| β-strand | 36-40 | 5 | 12 |
| β-strand | 43-47 | 5 | 12 |
| α-helix | 50-55 | 6 | |
| α-helix | 57-63 | 7 | |
| β-strand | 73-74 | 2 | 12 |
| α-helix | 81-93 | 13 | |
| β-strand | 96 | 1 | 13 |
| α-helix | 104-106 | 3 | |
Chain H: 33 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-32 | 15 | |
| α-helix | 44-53 | 10 | |
| α-helix | 86-103 | 18 | |
| α-helix | 115-136 | 22 | |
| α-helix | 138-139 | 2 | |
| α-helix | 140-145 | 6 | |
| α-helix | 146-149 | 4 | |
| α-helix | 159-171 | 13 | |
| α-helix | 178-187 | 10 | |
| α-helix | 198-210 | 13 | |
| α-helix | 227-228 | 2 | |
| α-helix | 229-233 | 5 | |
| α-helix | 234-254 | 21 | |
| α-helix | 260-277 | 18 | |
| α-helix | 284-295 | 12 | |
| α-helix | 300-312 | 13 | |
| α-helix | 316-328 | 13 | |
| α-helix | 334-355 | 22 | |
| α-helix | 363-384 | 22 | |
| α-helix | 389-404 | 16 | |
| α-helix | 407-412 | 6 | |
| α-helix | 417-429 | 13 | |
| α-helix | 439-453 | 15 | |
| α-helix | 459-475 | 17 | |
| α-helix | 482-495 | 14 | |
| α-helix | 499-526 | 28 | |
| β-strand | 534-536 | 3 | 15 |
| β-strand | 539-541 | 3 | 16 |
| α-helix | 554-556 | 3 | |
| α-helix | 560-573 | 14 | |
| β-strand | 577-581 | 5 | 16 |
| α-helix | 583-585 | 3 | |
| β-strand | 587 | 1 | 15 |
| β-strand | 589-591 | 3 | 17 |
| β-strand | 600-602 | 3 | 17 |
| α-helix | 605-612 | 8 | |
| α-helix | 613-615 | 3 | |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
Chain L: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-28 | 12 | |
| β-strand | 36-40 | 5 | 25 |
| β-strand | 43-47 | 5 | 25 |
| α-helix | 50-55 | 6 | |
| α-helix | 57-64 | 8 | |
| β-strand | 71-74 | 4 | 25 |
| α-helix | 81-93 | 13 | |
| β-strand | 98 | 1 | 13 |
| α-helix | 104-106 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-1 | A, H | protein | 764 | Homo sapiens | Q13616 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1, N-terminally processed | B, I | protein | 93 | Homo sapiens | P62877 (AlphaFold model) |
| S-phase kinase-associated protein 1 | C, G | protein | 162 | Homo sapiens | P63208 (AlphaFold model) |
| F-box/LRR-repeat protein 17 | D, K | protein | 392 | Homo sapiens | Q9UF56 (AlphaFold model) |
| Transcription regulator protein BACH1 | E, L | protein | 122 | Homo sapiens | O14867 |
Sequence of entity 1 (A, H), FASTA
>8UBU_1 Cullin-1 (chains A, H)
KQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKS
KKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKV
LNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERN
GETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFL
QQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHLEIFHTEFQNLLD
ADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAALNDPKMYVQTVLD
VHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPELLARYCDSLLKK
SSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMISKL
KQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCT
FALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILL
QYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLY
LGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLG
EVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (B, I), FASTA
>8UBU_2 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains B, I)
GAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVC
NHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 3 (C, G), FASTA
>8UBU_3 S-phase kinase-associated protein 1 (chains C, G)
MPSIKLQSSDGEIFEVDVEIAKQSTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVIQW
CTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVTCK
TVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK
Sequence of entity 4 (D, K), FASTA
>8UBU_4 F-box/LRR-repeat protein 17 (chains D, K)
CHREPPPETPDINQLPPSILLKIFSNLSLDERCLSASLVCKYWRDLCLDFQFWKQLDLSS
RQQVTDELLEKIASRSQNIIEINISDCRSMSDNGVCVLAFKCPGLLRYTAYRCKQLSDTS
IIAVASHCPLLQKVHVGNQDKLTDEGLKQLGSKCRELKDIHFGQCYKISDEGMIVIAKGC
LKLQRIYMQENKLVTDQSVKAFAEHCPELQYVGFMGCSVTSKGVIHLTKLRNLSSLDLRH
ITELDNETVMEIVKRCKNLSSLNLCLNWIINDRCVEVIAKEGQNLKELYLVSCKITDYAL
IAIGRYSMTIETVDVGWCKEITDQGATLIAQSSKSLRYLGLMRCDKVNEVTVEQLVQQYP
HITFSTVLQDCKRTLERAYQMGWTPNMSAASS
Sequence of entity 5 (E, L), FASTA
>8UBU_5 Transcription regulator protein BACH1 (chains E, L)
SVFAYESSVHSTNVLLSLNDQRKKDVLCDVTIFVEGQRFRAHRSVLAACSSYFHSRIVGQ
ADGELNITLPEEVTVKGFEPLIQFAYTAKLILSKENVDEVCKCVEFLSVHNIEESCFQFL
KF
Primary citation
Recognition of BACH1 quaternary structure degrons by two F-box proteins under oxidative stress. Cao, S., Garcia, S.F., Shi, H. et al. Cell (2024) 187:7568-7584.e22. DOI 10.1016/j.cell.2024.10.012 · 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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