8R5H: Cullin-2
Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2. Determined by electron microscopy at 3.44 Å resolution. Released 21 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.44 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 11,277
- Mol. weight
- 192.17 kDa
- Ligands
- ZN, 759, SY8
- Released
- 21 Feb 2024
Explore 8R5H in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8R5H contains 67 α-helices and 49 β-strands across 8 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: 36 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-25 | 16 | |
| α-helix | 32-46 | 15 | |
| α-helix | 55-75 | 21 | |
| α-helix | 83-104 | 22 | |
| α-helix | 106-107 | 2 | |
| α-helix | 108-113 | 6 | |
| α-helix | 139-150 | 12 | |
| α-helix | 153-154 | 2 | |
| α-helix | 155-159 | 5 | |
| α-helix | 160-170 | 11 | |
| α-helix | 178-187 | 10 | |
| α-helix | 201-203 | 3 | |
| α-helix | 204-208 | 5 | |
| α-helix | 209-228 | 20 | |
| α-helix | 232-253 | 22 | |
| α-helix | 259-267 | 9 | |
| α-helix | 268-272 | 5 | |
| α-helix | 273 | 1 | |
| α-helix | 275-277 | 3 | |
| α-helix | 282-287 | 6 | |
| α-helix | 291-301 | 11 | |
| α-helix | 308-327 | 20 | |
| α-helix | 337-357 | 21 | |
| α-helix | 362-376 | 15 | |
| α-helix | 387-399 | 13 | |
| α-helix | 408-422 | 15 | |
| α-helix | 428-443 | 16 | |
| α-helix | 451-464 | 14 | |
| α-helix | 467-469 | 3 | |
| α-helix | 471-493 | 23 | |
| β-strand | 506-513 | 8 | 1 |
| α-helix | 528-530 | 3 | |
| α-helix | 531-533 | 3 | |
| α-helix | 535-547 | 13 | |
| β-strand | 552-555 | 4 | 1 |
| β-strand | 561-566 | 6 | 1 |
| β-strand | 574-578 | 5 | 1 |
| α-helix | 579-587 | 9 | |
| β-strand | 593-595 | 3 | 2 |
| α-helix | 596-603 | 8 | |
| α-helix | 607-619 | 13 | |
| β-strand | 623-625 | 3 | 2 |
| β-strand | 637-640 | 4 | 2 |
| β-strand | 650-652 | 3 | 1 |
Chain C: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-20 | 13 | |
| β-strand | 40 | 1 | 4 |
| β-strand | 60-63 | 4 | 4 |
| β-strand | 74-77 | 4 | 4 |
| β-strand | 86 | 1 | 5 |
| β-strand | 92 | 1 | 5 |
| α-helix | 120-132 | 13 | |
| α-helix | 142-154 | 13 | |
| α-helix | 160-179 | 20 | |
Chain D: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 8 |
| β-strand | 28-32 | 5 | 8 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 59-61 | 3 | 8 |
| α-helix | 67-82 | 16 | |
| α-helix | 91-94 | 4 | |
| α-helix | 100-110 | 11 | |
Chain F: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 350-364 | 15 | |
| α-helix | 375-377 | 3 | |
| α-helix | 382-385 | 4 | |
| α-helix | 390-393 | 4 | |
| α-helix | 400-407 | 8 | |
| α-helix | 415-432 | 18 | |
| α-helix | 438-455 | 18 | |
Chain G: 4 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 8 |
| β-strand | 10 | 1 | 9 |
| β-strand | 12-18 | 7 | 8 |
| β-strand | 23 | 1 | 10 |
| α-helix | 24-35 | 12 | |
| β-strand | 43-46 | 4 | 8 |
| β-strand | 49-50 | 2 | 8 |
| β-strand | 56 | 1 | 10 |
| α-helix | 57-60 | 4 | |
| β-strand | 75-78 | 4 | 8 |
| β-strand | 80-81 | 2 | 11 |
| β-strand | 84-85 | 2 | 11 |
| α-helix | 86-88 | 3 | |
| β-strand | 90 | 1 | 9 |
| α-helix | 98-100 | 3 | |
Chain H: 5 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 71-77 | 7 | 12 |
| β-strand | 84-88 | 5 | 13 |
| β-strand | 96-97 | 2 | 13 |
| β-strand | 101 | 1 | 13 |
| β-strand | 106-112 | 7 | 12 |
| β-strand | 117-121 | 5 | 13 |
| β-strand | 127 | 1 | 13 |
| β-strand | 129-130 | 2 | 14 |
| β-strand | 133 | 1 | 14 |
| β-strand | 136 | 1 | 13 |
| α-helix | 146 | 1 | |
| β-strand | 147-149 | 3 | 12 |
| β-strand | 151-152 | 2 | 14 |
| α-helix | 158-169 | 12 | |
| α-helix | 175-177 | 3 | |
| α-helix | 182-189 | 8 | |
| α-helix | 194-208 | 15 | |
Chain R: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-34 | 13 | 1 |
| β-strand | 41 | 1 | 3 |
| β-strand | 48 | 1 | 3 |
| α-helix | 54-57 | 4 | |
| α-helix | 81-88 | 8 | |
Chain U: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 6 |
| β-strand | 12-16 | 5 | 6 |
| β-strand | 22 | 1 | 7 |
| α-helix | 23-33 | 11 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-44 | 3 | 6 |
| β-strand | 49 | 1 | 6 |
| α-helix | 50-51 | 2 | |
| β-strand | 55 | 1 | 7 |
| α-helix | 56-59 | 4 | |
| β-strand | 66-70 | 5 | 6 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-2 | A | protein | 745 | Homo sapiens | Q13617 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1, N-terminally processed | R | protein | 104 | Homo sapiens | P62877 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 R2 | C | protein | 238 | Homo sapiens | Q712K3 (AlphaFold model) |
| Ubiquitin | U | protein | 75 | Homo sapiens | P0CG48 (AlphaFold model) |
| Elongin-C | D | protein | 112 | Homo sapiens | Q15369 |
| Bromodomain-containing protein 4 | F | protein | 115 | Homo sapiens | O60885 |
| Elongin-B | G | protein | 118 | Homo sapiens | Q15370 |
| von Hippel-Lindau disease tumor suppressor | H | protein | 160 | Homo sapiens | P40337 |
Sequence of entity 1 (A), FASTA
>8R5H_1 Cullin-2 (chains A)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 2 (R), FASTA
>8R5H_2 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains R)
MDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASAT
SEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 3 (C), FASTA
>8R5H_3 Ubiquitin-conjugating enzyme E2 R2 (chains C)
MAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKA
HIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVCISILHPPVDDPQSGELPSERWNPTQNV
RTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDG
VKVPTTLAEYCIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 4 (U), FASTA
>8R5H_4 Ubiquitin (chains U)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
Sequence of entity 5 (D), FASTA
>8R5H_5 Elongin-C (chains D)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 6 (F), FASTA
>8R5H_6 Bromodomain-containing protein 4 (chains F)
KSSKVSEQLKAASGILKEMFAKCHAAYAWPFYKPVDVEALGLHDYADIIKHPMDMSTIKS
KLEAREYRDAQEFGADVRLMFSNAYKYNPPDHEVVAMARKLQDVFEMRFAKMPDE
Sequence of entity 7 (G), FASTA
>8R5H_7 Elongin-B (chains G)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Sequence of entity 8 (H), FASTA
>8R5H_8 von Hippel-Lindau disease tumor suppressor (chains H)
MEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYR
GHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPE
NYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 3 |
| 759 | (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-tr… | C49 H60 Cl N9 O8 S2 | 1 |
| SY8 | 5-azanylpentan-2-one | C5 H11 N O | 1 |
Primary citation
Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Li, J., Purser, N., Liwocha, J. et al. Mol Cell (2024) 84:1304. DOI 10.1016/j.molcel.2024.01.022 · PubMed
Other PDB entries of the same protein (UniProt Q13617 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7PLO 2.8 Å, H. sapiens replisome-CUL2/LRR1 complex
- 9EFQ 2.96 Å, Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2
- 4WQO 3.2 Å, Structure of VHL-EloB-EloC-Cul2
- 8JAU 3.22 Å, Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer)
- 8JAQ 3.26 Å, Structure of CRL2APPBP2 bound with RxxGP degron (tetramer)
- 8WQF 3.27 Å, cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
- 9UA3 3.28 Å, Cryo-EM structure of neddylated CUL2-RBX1-FEM1C-ELOB-ELOC
- 8JAL 3.3 Å, Structure of CRL2APPBP2 bound with RxxGP degron (dimer)
- 8JAR 3.3 Å, Structure of CRL2APPBP2 bound with RxxGPAA degron (dimer)
- 8WQB 3.37 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89…
- 8WQE 3.38 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1…
- 8WQA 3.39 Å, Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89…
Browse structure collections
About this viewer
MolViewer shows 8R5H directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.