8WQC: Neddylated CUL2-RBX1-ELOB-ELOC-FEM1B
cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1. Determined by electron microscopy at 3.54 Å resolution. Released 3 Apr 2024.
- Method
- Electron microscopy
- Resolution
- 3.54 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 26,832
- Mol. weight
- 402.86 kDa
- Ligands
- ZN
- Released
- 3 Apr 2024
Explore 8WQC in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WQC contains 163 α-helices and 90 β-strands across 12 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: 35 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 18-24 | 7 | |
| α-helix | 29-35 | 7 | |
| β-strand | 40-42 | 3 | 32 |
| β-strand | 45-47 | 3 | 32 |
| α-helix | 49-55 | 7 | |
| α-helix | 59-64 | 6 | |
| α-helix | 65-69 | 5 | |
| β-strand | 77-80 | 4 | 33 |
| β-strand | 85-89 | 5 | 33 |
| α-helix | 91-97 | 7 | |
| α-helix | 101-110 | 10 | |
| α-helix | 124-131 | 8 | |
| α-helix | 134-142 | 9 | |
| α-helix | 157-163 | 7 | |
| α-helix | 167-175 | 9 | |
| α-helix | 190-197 | 8 | |
| α-helix | 200-208 | 9 | |
| α-helix | 222-228 | 7 | |
| α-helix | 232-238 | 7 | |
| α-helix | 247-261 | 15 | |
| α-helix | 269-283 | 15 | |
| α-helix | 295-298 | 4 | |
| α-helix | 300-302 | 3 | |
| α-helix | 311-316 | 6 | |
| α-helix | 321-336 | 16 | |
| α-helix | 344-356 | 13 | |
| α-helix | 360-375 | 16 | |
| α-helix | 383-397 | 15 | |
| α-helix | 404-427 | 24 | |
| α-helix | 433-454 | 22 | |
| α-helix | 461-476 | 16 | |
| α-helix | 487-491 | 5 | |
| α-helix | 512-520 | 9 | |
| α-helix | 535-539 | 5 | |
| α-helix | 550-559 | 10 | |
| α-helix | 583-592 | 10 | |
| α-helix | 597-606 | 10 | |
| α-helix | 618-626 | 9 | |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 1 |
| β-strand | 29-32 | 4 | 1 |
| α-helix | 33-36 | 4 | |
| α-helix | 41-45 | 5 | |
| β-strand | 60-61 | 2 | 1 |
| α-helix | 67-83 | 17 | |
| α-helix | 91-93 | 3 | |
| α-helix | 100-109 | 10 | |
Chain C: 37 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-24 | 15 | |
| α-helix | 32-46 | 15 | |
| α-helix | 54-78 | 25 | |
| α-helix | 83-87 | 5 | |
| α-helix | 92-104 | 13 | |
| α-helix | 106-108 | 3 | |
| α-helix | 109-113 | 5 | |
| α-helix | 139-149 | 11 | |
| α-helix | 157-172 | 16 | |
| α-helix | 178-185 | 8 | |
| α-helix | 191-194 | 4 | |
| α-helix | 203-206 | 4 | |
| α-helix | 208-229 | 22 | |
| α-helix | 232-251 | 20 | |
| α-helix | 256-259 | 4 | |
| α-helix | 263-270 | 8 | |
| α-helix | 272-274 | 3 | |
| α-helix | 275-287 | 13 | |
| α-helix | 291-302 | 12 | |
| α-helix | 308-326 | 19 | |
| α-helix | 335-357 | 23 | |
| α-helix | 362-376 | 15 | |
| α-helix | 387-399 | 13 | |
| β-strand | 400 | 1 | 11 |
| α-helix | 408-422 | 15 | |
| α-helix | 428-444 | 17 | |
| β-strand | 448 | 1 | 11 |
| α-helix | 451-465 | 15 | |
| α-helix | 469-471 | 3 | |
| α-helix | 473-488 | 16 | |
| α-helix | 491-495 | 5 | |
| β-strand | 508-513 | 6 | 12 |
| α-helix | 534-546 | 13 | |
| β-strand | 551-555 | 5 | 12 |
| β-strand | 561-565 | 5 | 12 |
| β-strand | 574-578 | 5 | 12 |
| α-helix | 580-583 | 4 | |
| β-strand | 593-594 | 2 | 13 |
| α-helix | 596-602 | 7 | |
| α-helix | 607-619 | 13 | |
| β-strand | 623-625 | 3 | 13 |
| β-strand | 638-640 | 3 | 13 |
| β-strand | 650-652 | 3 | 12 |
| α-helix | 665-691 | 27 | |
| β-strand | 694 | 1 | 14 |
| α-helix | 696-706 | 11 | |
| α-helix | 715-722 | 8 | |
| α-helix | 724-728 | 5 | |
| β-strand | 733 | 1 | 14 |
| β-strand | 741 | 1 | 14 |
Chain D: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-9 | 7 | 1 |
| β-strand | 10 | 1 | 2 |
| β-strand | 12-18 | 7 | 1 |
| β-strand | 23 | 1 | 3 |
| α-helix | 24-35 | 12 | |
| α-helix | 39-41 | 3 | |
| β-strand | 42-43 | 2 | 4 |
| β-strand | 45-46 | 2 | 5 |
| β-strand | 49-50 | 2 | 5 |
| β-strand | 56 | 1 | 3 |
| β-strand | 68 | 1 | 6 |
| β-strand | 71 | 1 | 6 |
| β-strand | 73-76 | 4 | 1 |
| β-strand | 78-79 | 2 | 4 |
| β-strand | 90 | 1 | 2 |
| α-helix | 94-96 | 3 | |
Chain E: 34 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-25 | 16 | |
| α-helix | 32-47 | 16 | |
| α-helix | 54-78 | 25 | |
| α-helix | 84-104 | 21 | |
| α-helix | 106-109 | 4 | |
| α-helix | 112-115 | 4 | |
| α-helix | 139-147 | 9 | |
| α-helix | 148-152 | 5 | |
| α-helix | 158-171 | 14 | |
| α-helix | 178-186 | 9 | |
| α-helix | 191-193 | 3 | |
| α-helix | 208-229 | 22 | |
| α-helix | 232-253 | 22 | |
| α-helix | 256-258 | 3 | |
| α-helix | 261-270 | 10 | |
| α-helix | 275-287 | 13 | |
| α-helix | 291-303 | 13 | |
| α-helix | 307-326 | 20 | |
| α-helix | 335-356 | 22 | |
| α-helix | 362-376 | 15 | |
| α-helix | 387-399 | 13 | |
| β-strand | 400 | 1 | 19 |
| α-helix | 408-422 | 15 | |
| α-helix | 428-435 | 8 | |
| α-helix | 440-444 | 5 | |
| β-strand | 448 | 1 | 19 |
| α-helix | 453-462 | 10 | |
| α-helix | 472-494 | 23 | |
| β-strand | 510-513 | 4 | 8 |
| α-helix | 534-546 | 13 | |
| β-strand | 551-553 | 3 | 8 |
| β-strand | 562-564 | 3 | 7 |
| β-strand | 575-577 | 3 | 7 |
| α-helix | 580-583 | 4 | |
| α-helix | 587-590 | 4 | |
| β-strand | 594-595 | 2 | 20 |
| α-helix | 598-601 | 4 | |
| α-helix | 607-620 | 14 | |
| β-strand | 623-625 | 3 | 20 |
| β-strand | 637-640 | 4 | 20 |
| α-helix | 665-688 | 24 | |
| α-helix | 698-706 | 9 | |
| α-helix | 715-727 | 13 | |
| β-strand | 731-733 | 3 | 21 |
| β-strand | 741-743 | 3 | 21 |
Chain F: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24-27 | 4 | 7 |
| β-strand | 30-35 | 6 | 8 |
| β-strand | 41 | 1 | 9 |
| β-strand | 48 | 1 | 9 |
| α-helix | 60-63 | 4 | |
| β-strand | 70-72 | 3 | 10 |
| β-strand | 78-80 | 3 | 10 |
| α-helix | 81-87 | 7 | |
Chain G: 34 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 18-23 | 6 | |
| α-helix | 29-35 | 7 | |
| β-strand | 40-42 | 3 | 34 |
| β-strand | 45-47 | 3 | 34 |
| α-helix | 49-55 | 7 | |
| α-helix | 59-63 | 5 | |
| α-helix | 64-69 | 6 | |
| β-strand | 77-80 | 4 | 35 |
| β-strand | 85-89 | 5 | 35 |
| α-helix | 91-97 | 7 | |
| α-helix | 101-110 | 10 | |
| α-helix | 124-131 | 8 | |
| α-helix | 134-142 | 9 | |
| α-helix | 157-163 | 7 | |
| α-helix | 167-175 | 9 | |
| α-helix | 190-197 | 8 | |
| α-helix | 200-208 | 9 | |
| α-helix | 222-228 | 7 | |
| α-helix | 232-235 | 4 | |
| α-helix | 247-261 | 15 | |
| α-helix | 269-283 | 15 | |
| α-helix | 295-298 | 4 | |
| α-helix | 311-316 | 6 | |
| α-helix | 321-336 | 16 | |
| α-helix | 344-356 | 13 | |
| α-helix | 360-376 | 17 | |
| α-helix | 383-397 | 15 | |
| α-helix | 404-427 | 24 | |
| α-helix | 433-454 | 22 | |
| α-helix | 461-476 | 16 | |
| α-helix | 487-491 | 5 | |
| α-helix | 512-520 | 9 | |
| α-helix | 535-539 | 5 | |
| α-helix | 550-559 | 10 | |
| α-helix | 583-592 | 10 | |
| α-helix | 597-608 | 12 | |
| α-helix | 618-626 | 9 | |
Chain H: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 25 |
| β-strand | 28-32 | 5 | 25 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-45 | 6 | |
| β-strand | 60-61 | 2 | 25 |
| α-helix | 67-83 | 17 | |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Elongin-B | D, I | protein | 118 | Homo sapiens | Q15370 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1, N-terminally processed | F, J | protein | 96 | Homo sapiens | P62877 (AlphaFold model) |
| Elongin-C | B, H | protein | 96 | Homo sapiens | Q15369 (AlphaFold model) |
| Cullin-2 | C, E | protein | 750 | Homo sapiens | Q13617 (AlphaFold model) |
| NEDD8 | K, N | protein | 76 | Homo sapiens | Q15843 |
| Protein fem-1 homolog B | A, G | protein | 627 | Homo sapiens | Q9UK73 |
Sequence of entity 1 (D, I), FASTA
>8WQC_1 Elongin-B (chains D, I)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Sequence of entity 2 (F, J), FASTA
>8WQC_2 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains F, J)
SHMGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW
GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 3 (B, H), FASTA
>8WQC_3 Elongin-C (chains B, H)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 4 (C, E), FASTA
>8WQC_4 Cullin-2 (chains C, E)
SASWSHPQFEKGGGSGGGSGTSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFS
DIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADY
MDCLYRYLNTQFIKKNGGGPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGED
PNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQY
MEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMA
NMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLIN
TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRL
TSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHR
MYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEK
SVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVS
YKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITT
SMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSI
SMIKKCIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 5 (K, N), FASTA
>8WQC_5 NEDD8 (chains K, N)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG
Sequence of entity 6 (A, G), FASTA
>8WQC_6 Protein fem-1 homolog B (chains A, G)
MEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAK
VVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVT
NSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADP
NAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLS
HADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIH
AYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADNMEF
EQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLEIEQ
SMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHLDPR
TREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALHIIV
QYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSLKCL
AARAVRANDINYQDQIPRTLEEFVGFH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 6 |
Primary citation
Mechanism of Psi-Pro/C-degron recognition by the CRL2 FEM1B ubiquitin ligase. Chen, X., Raiff, A., Li, S. et al. Nat Commun (2024) 15:3558-3558. DOI 10.1038/s41467-024-47890-5 · PubMed
Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
- 9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
- 7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
- 8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
- 4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
- 6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
- 6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
- 7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
- 6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
- 8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
- 6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
- 1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex
Browse structure collections
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