7B5N: Cullin-1
Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Determined by electron microscopy at 3.6 Å resolution. Released 10 Feb 2021.
- Method
- Electron microscopy
- Resolution
- 3.6 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 9,965
- Mol. weight
- 202.41 kDa
- Ligands
- ZN, SY8
- Released
- 10 Feb 2021
Explore 7B5N in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7B5N contains 42 α-helices and 53 β-strands across 6 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: 19 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 337-353 | 17 | |
| α-helix | 357-360 | 4 | |
| α-helix | 363-383 | 21 | |
| α-helix | 389-404 | 16 | |
| α-helix | 407-412 | 6 | |
| α-helix | 418-430 | 13 | |
| α-helix | 436-438 | 3 | |
| α-helix | 439-455 | 17 | |
| α-helix | 461-475 | 15 | |
| α-helix | 482-496 | 15 | |
| α-helix | 502-525 | 24 | |
| β-strand | 534-540 | 7 | 1 |
| α-helix | 560-573 | 14 | |
| β-strand | 580-589 | 10 | 1 |
| β-strand | 604 | 1 | 1 |
| α-helix | 605-613 | 9 | |
| β-strand | 619-621 | 3 | 2 |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
| β-strand | 649-650 | 2 | 2 |
| β-strand | 668-671 | 4 | 2 |
| α-helix | 706-721 | 16 | |
| β-strand | 725 | 1 | 3 |
| α-helix | 727-737 | 11 | |
| α-helix | 746-758 | 13 | |
| β-strand | 762-764 | 3 | 3 |
| α-helix | 765 | 1 | |
| β-strand | 772-774 | 3 | 3 |
Chain D: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-17 | 16 | |
| β-strand | 22-27 | 6 | 18 |
| β-strand | 34-39 | 6 | 18 |
| β-strand | 50 | 1 | 19 |
| β-strand | 51-56 | 6 | 18 |
| β-strand | 67-69 | 3 | 18 |
| α-helix | 101-113 | 13 | |
| α-helix | 123-131 | 9 | |
| α-helix | 133-147 | 15 | |
| β-strand | 149 | 1 | 19 |
Chain H: 15 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 101 | 1 | 4 |
| β-strand | 104 | 1 | 5 |
| α-helix | 106-124 | 19 | |
| α-helix | 128-137 | 10 | |
| α-helix | 142-149 | 8 | |
| α-helix | 155-161 | 7 | |
| α-helix | 195-197 | 3 | |
| β-strand | 199 | 1 | 6 |
| β-strand | 207 | 1 | 6 |
| α-helix | 209-222 | 14 | |
| β-strand | 230 | 1 | 7 |
| β-strand | 239 | 1 | 7 |
| α-helix | 242-248 | 7 | |
| α-helix | 253-269 | 17 | |
| β-strand | 275 | 1 | 5 |
| β-strand | 284 | 1 | 5 |
| β-strand | 287 | 1 | 4 |
| β-strand | 294-296 | 3 | 8 |
| β-strand | 302-304 | 3 | 8 |
| β-strand | 310 | 1 | 8 |
| α-helix | 317-325 | 9 | |
| α-helix | 333-340 | 8 | |
| β-strand | 342-343 | 2 | 9 |
| β-strand | 350-351 | 2 | 9 |
| β-strand | 361 | 1 | 10 |
| β-strand | 370 | 1 | 10 |
| β-strand | 371 | 1 | 11 |
| β-strand | 378 | 1 | 11 |
| 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 N: 2 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 13 |
| β-strand | 12-16 | 5 | 13 |
| β-strand | 22 | 1 | 14 |
| α-helix | 23-34 | 12 | |
| β-strand | 42-43 | 2 | 15 |
| β-strand | 44-45 | 2 | 16 |
| β-strand | 48-49 | 2 | 16 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 14 |
| β-strand | 66 | 1 | 13 |
| β-strand | 69-70 | 2 | 15 |
Chain R: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 26-32 | 7 | 1 |
| β-strand | 70-73 | 4 | 17 |
| β-strand | 78-80 | 3 | 17 |
| α-helix | 81-90 | 10 | |
| β-strand | 103-105 | 3 | 17 |
Chain U: 1 helix, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-7 | 6 | 9 |
| β-strand | 10-16 | 7 | 9 |
| β-strand | 22 | 1 | 12 |
| α-helix | 23-33 | 11 | |
| β-strand | 41-45 | 5 | 9 |
| β-strand | 48-49 | 2 | 9 |
| β-strand | 55 | 1 | 12 |
| β-strand | 66-71 | 6 | 9 |
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) |
| Polyubiquitin-C | U | protein | 75 | Homo sapiens | P0CG48 (AlphaFold model) |
| NEDD8 | N | protein | 81 | Homo sapiens | Q15843 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1 | R | protein | 108 | Homo sapiens | P62877 |
| Ubiquitin-conjugating enzyme E2 L3 | D | protein | 154 | Homo sapiens | P68036 |
Sequence of entity 1 (C), FASTA
>7B5N_1 Cullin-1 (chains C)
MSSTRSQNPHGLKQIGLDQIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSN
QARGAGVPPSKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYT
QQWEDYRFSSKVLNGICAYLNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVT
NAVLKLIEKERNGETINTRLISGVVQSYVELGLNEDDAFAKGPTLTVYKESFESQFLADT
ERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYLHESTQDELARKCEQVLIEKHL
EIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGLAAIEKCGEAAL
NDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSPE
LLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSA
SDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVL
SSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYT
LQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKLLVLEDENANVDE
VELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETTHKNIEEDRKLLIQAAIVRIMK
MRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA
Sequence of entity 2 (H), FASTA
>7B5N_2 E3 ubiquitin-protein ligase ARIH1 (chains H)
MDSDEGYNYEFDEDEECSEEDSGAEEEEDEDDDEPDDDTLDLGEVELVEPGLGVGGERDG
LLCGETGGGGGSALGPGGGGGGGGGGGGGGPGHEQEEDYRYEVLTAEQILQHMVECIREV
NEVIQNPATITRILLSHFNWDKEKLMERYFDGNLEKLFAECHVINPSKKSRTRQMNTRSS
AQDMPCQICYLNYPNSYFTGLECGHKFCMQCWSEYLTTKIMEEGMGQTISCPAHGCDILV
DDNTVMRLITDSKVKLKYQHLITNSFVECNRLLKWCPAPDCHHVVKVQYPDAKPVRCKCG
RQFCFNCGENWHDPVKCKWLKKWIKKCDDDSETSNWIAANTKECPKCHVTIEKDGGCNHM
VCRNQNCKAEFCWVCLGPWEPHGSAWYNCNRYNEDDAKAARDAQERSRAALQRYLFYCNR
YMNHMQSLRFEHKLYAQVKQKMEEMQQHNMSWIEVQFLKKAVDVLCQCRATLMYTYVFAF
YLKKNNQSIIFENNQADLENATEVLSGYLERDISQDSLQDIKQKVQDKYRYCESRRRVLL
QHVHEGYEKDLWEYIED
Sequence of entity 3 (U), FASTA
>7B5N_3 Polyubiquitin-C (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
Sequence of entity 4 (N), FASTA
>7B5N_4 NEDD8 (chains N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGGGGLRQ
Sequence of entity 5 (R), FASTA
>7B5N_5 E3 ubiquitin-protein ligase RBX1 (chains R)
MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQ
ASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 6 (D), FASTA
>7B5N_6 Ubiquitin-conjugating enzyme E2 L3 (chains D)
MAASRRLMKELEEIRKAGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINFPAE
YPFKPPKITFKTKIYHPNIDEKGQVCLPVISAENWKPATKTDQVIQSLIALVNDPQPEHP
LRADLAEEYSKDRKKFAKNAEEFTKKYGEKRPVD
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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