8WQH: Neddylated CUL2-RBX1-ELOB-ELOC-FEM1B
cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2). Determined by electron microscopy at 3.44 Å resolution. Released 3 Apr 2024.
- Method
- Electron microscopy
- Resolution
- 3.44 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 24,811
- Mol. weight
- 392.16 kDa
- Ligands
- ZN
- Released
- 3 Apr 2024
Explore 8WQH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8WQH contains 169 α-helices and 71 β-strands across 11 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, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-24 | 11 | |
| α-helix | 32-46 | 15 | |
| α-helix | 54-78 | 25 | |
| α-helix | 83-104 | 22 | |
| α-helix | 106-107 | 2 | |
| α-helix | 108-113 | 6 | |
| α-helix | 139-145 | 7 | |
| α-helix | 153-155 | 3 | |
| α-helix | 156-172 | 17 | |
| α-helix | 178-190 | 13 | |
| α-helix | 199-201 | 3 | |
| α-helix | 202-203 | 2 | |
| α-helix | 204-208 | 5 | |
| α-helix | 209-228 | 20 | |
| α-helix | 232-249 | 18 | |
| α-helix | 256-258 | 3 | |
| α-helix | 259-267 | 9 | |
| α-helix | 268-272 | 5 | |
| α-helix | 275-280 | 6 | |
| α-helix | 282-287 | 6 | |
| α-helix | 291-301 | 11 | |
| α-helix | 308-324 | 17 | |
| α-helix | 335-356 | 22 | |
| α-helix | 362-376 | 15 | |
| α-helix | 379-380 | 2 | |
| α-helix | 387-399 | 13 | |
| β-strand | 400 | 1 | 8 |
| α-helix | 408-416 | 9 | |
| α-helix | 418-422 | 5 | |
| α-helix | 428-444 | 17 | |
| β-strand | 448 | 1 | 8 |
| α-helix | 451-464 | 14 | |
| α-helix | 472-481 | 10 | |
| α-helix | 484-495 | 12 | |
| β-strand | 506-513 | 8 | 9 |
| β-strand | 514 | 1 | 10 |
| β-strand | 517 | 1 | 10 |
| α-helix | 531-546 | 16 | |
| β-strand | 552-565 | 14 | 9 |
| β-strand | 574 | 1 | 9 |
| β-strand | 577-578 | 2 | 9 |
| α-helix | 579-590 | 12 | |
| β-strand | 594 | 1 | 11 |
| α-helix | 596-603 | 8 | |
| α-helix | 607-620 | 14 | |
| β-strand | 623-625 | 3 | 11 |
| β-strand | 638-640 | 3 | 11 |
Chain B: 3 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-34 | 12 | 9 |
| β-strand | 42 | 1 | 12 |
| β-strand | 47 | 1 | 12 |
| α-helix | 52-53 | 2 | |
| α-helix | 54-57 | 4 | |
| β-strand | 70-72 | 3 | 13 |
| β-strand | 73 | 1 | 14 |
| β-strand | 78-80 | 3 | 13 |
| α-helix | 81-88 | 8 | |
| β-strand | 93 | 1 | 15 |
| β-strand | 100 | 1 | 15 |
| β-strand | 103 | 1 | 14 |
Chain C: 32 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-25 | 16 | |
| α-helix | 32-46 | 15 | |
| α-helix | 54-66 | 13 | |
| α-helix | 69-78 | 10 | |
| α-helix | 83-104 | 22 | |
| α-helix | 106-108 | 3 | |
| α-helix | 109-113 | 5 | |
| α-helix | 139-145 | 7 | |
| α-helix | 147 | 1 | |
| α-helix | 148-152 | 5 | |
| α-helix | 156-171 | 16 | |
| α-helix | 178-190 | 13 | |
| α-helix | 201-203 | 3 | |
| α-helix | 204-208 | 5 | |
| α-helix | 209-227 | 19 | |
| α-helix | 232-249 | 18 | |
| α-helix | 256-258 | 3 | |
| α-helix | 259-270 | 12 | |
| α-helix | 275-286 | 12 | |
| α-helix | 291-303 | 13 | |
| α-helix | 308-327 | 20 | |
| α-helix | 335-356 | 22 | |
| α-helix | 362-376 | 15 | |
| α-helix | 387-399 | 13 | |
| β-strand | 400 | 1 | 1 |
| α-helix | 408-422 | 15 | |
| α-helix | 428-444 | 17 | |
| β-strand | 448 | 1 | 1 |
| α-helix | 451-469 | 19 | |
| α-helix | 472-496 | 25 | |
| β-strand | 506-513 | 8 | 2 |
| α-helix | 531-547 | 17 | |
| β-strand | 551-555 | 5 | 2 |
| β-strand | 561-565 | 5 | 2 |
| β-strand | 574-578 | 5 | 2 |
| α-helix | 579-590 | 12 | |
| β-strand | 593-594 | 2 | 3 |
| α-helix | 596-603 | 8 | |
| α-helix | 607-618 | 12 | |
| β-strand | 623-625 | 3 | 3 |
| β-strand | 638-640 | 3 | 3 |
| β-strand | 650-652 | 3 | 2 |
Chain D: 36 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 17-24 | 8 | |
| α-helix | 29-35 | 7 | |
| β-strand | 40-42 | 3 | 20 |
| β-strand | 45-47 | 3 | 20 |
| α-helix | 49-55 | 7 | |
| α-helix | 59-67 | 9 | |
| β-strand | 78-79 | 2 | 21 |
| β-strand | 86-87 | 2 | 21 |
| α-helix | 91-97 | 7 | |
| α-helix | 101-110 | 10 | |
| α-helix | 124-131 | 8 | |
| α-helix | 134-142 | 9 | |
| α-helix | 157-162 | 6 | |
| 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 | 238-241 | 4 | |
| α-helix | 247-261 | 15 | |
| α-helix | 269-284 | 16 | |
| α-helix | 295-299 | 5 | |
| α-helix | 311-316 | 6 | |
| α-helix | 317-319 | 3 | |
| α-helix | 321-336 | 16 | |
| α-helix | 344-355 | 12 | |
| α-helix | 361-376 | 16 | |
| α-helix | 382-397 | 16 | |
| α-helix | 404-427 | 24 | |
| α-helix | 433-455 | 23 | |
| α-helix | 461-477 | 17 | |
| α-helix | 487-492 | 6 | |
| α-helix | 503-506 | 4 | |
| α-helix | 512-520 | 9 | |
| α-helix | 535-540 | 6 | |
| α-helix | 549-562 | 14 | |
| α-helix | 583-590 | 8 | |
| α-helix | 597-608 | 12 | |
| α-helix | 618-626 | 9 | |
Chain E: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 16 |
| β-strand | 29-32 | 4 | 16 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-45 | 6 | |
| β-strand | 59-61 | 3 | 16 |
| α-helix | 67-82 | 16 | |
| α-helix | 90-93 | 4 | |
| α-helix | 103-109 | 7 | |
Chain F: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 16 |
| β-strand | 13-18 | 6 | 16 |
| β-strand | 23 | 1 | 17 |
| α-helix | 24-35 | 12 | |
| α-helix | 39-41 | 3 | |
| β-strand | 42-44 | 3 | 18 |
| β-strand | 45 | 1 | 19 |
| β-strand | 50 | 1 | 19 |
| β-strand | 56 | 1 | 17 |
| α-helix | 72 | 1 | |
| β-strand | 73-75 | 3 | 16 |
| β-strand | 77-79 | 3 | 18 |
| α-helix | 86-88 | 3 | |
| α-helix | 90-92 | 3 | |
| α-helix | 94-99 | 6 | |
Chain H: 38 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 17-24 | 8 | |
| α-helix | 29-35 | 7 | |
| β-strand | 40-42 | 3 | 27 |
| β-strand | 45-47 | 3 | 27 |
| α-helix | 49-55 | 7 | |
| α-helix | 59-68 | 10 | |
| α-helix | 91-98 | 8 | |
| α-helix | 101-109 | 9 | |
| α-helix | 124-131 | 8 | |
| α-helix | 134-142 | 9 | |
| α-helix | 157-162 | 6 | |
| α-helix | 167-175 | 9 | |
| α-helix | 190-196 | 7 | |
| α-helix | 200-208 | 9 | |
| α-helix | 222-228 | 7 | |
| α-helix | 232-235 | 4 | |
| α-helix | 239-241 | 3 | |
| α-helix | 247-260 | 14 | |
| α-helix | 269-283 | 15 | |
| α-helix | 295-297 | 3 | |
| α-helix | 311-316 | 6 | |
| α-helix | 321-336 | 16 | |
| α-helix | 344-354 | 11 | |
| α-helix | 355-357 | 3 | |
| α-helix | 361-376 | 16 | |
| α-helix | 382-397 | 16 | |
| α-helix | 400-403 | 4 | |
| α-helix | 404-427 | 24 | |
| α-helix | 433-455 | 23 | |
| α-helix | 461-477 | 17 | |
| α-helix | 487-492 | 6 | |
| α-helix | 503-506 | 4 | |
| α-helix | 512-520 | 9 | |
| α-helix | 535-539 | 5 | |
| α-helix | 549-561 | 13 | |
| α-helix | 578-580 | 3 | |
| α-helix | 583-590 | 8 | |
| α-helix | 597-607 | 11 | |
| α-helix | 618-626 | 9 | |
Chain I: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-19 | 2 | 22 |
| β-strand | 20-22 | 3 | 23 |
| β-strand | 28 | 1 | 23 |
| β-strand | 31-32 | 2 | 22 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 59-61 | 3 | 23 |
| α-helix | 67-82 | 16 | |
| α-helix | 91-93 | 3 | |
| α-helix | 97-109 | 13 | |
3 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 |
|---|
| Cullin-2 | A, C | protein | 750 | Homo sapiens | Q13617 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1, N-terminally processed | B, J | protein | 96 | Homo sapiens | P62877 (AlphaFold model) |
| Elongin-C | E, I | protein | 96 | Homo sapiens | Q15369 (AlphaFold model) |
| Elongin-B | F, K | protein | 118 | Homo sapiens | Q15370 (AlphaFold model) |
| Protein fem-1 homolog B | D, H | protein | 627 | Homo sapiens | Q9UK73 |
| Coiled-coil domain-containing protein 89 | G, L | protein | 31 | Homo sapiens | Q8N998 |
Sequence of entity 1 (A, C), FASTA
>8WQH_1 Cullin-2 (chains A, C)
SASWSHPQFEKGGGSGGGSGTSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFS
DIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADY
MDCLYRYLNTQFIKKNGGGPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGED
PNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQY
MEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMA
NMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLIN
TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRL
TSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHR
MYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEK
SVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVS
YKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITT
SMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSI
SMIKKCIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 2 (B, J), FASTA
>8WQH_2 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains B, J)
SHMGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW
GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 3 (E, I), FASTA
>8WQH_3 Elongin-C (chains E, I)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 4 (F, K), FASTA
>8WQH_4 Elongin-B (chains F, K)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ
Sequence of entity 5 (D, H), FASTA
>8WQH_5 Protein fem-1 homolog B (chains D, H)
MEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAK
VVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVT
NSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADP
NAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLS
HADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIH
AYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADNMEF
EQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLEIEQ
SMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHLDPR
TREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALHIIV
QYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSLKCL
AARAVRANDINYQDQIPRTLEEFVGFH
Sequence of entity 6 (G, L), FASTA
>8WQH_6 Coiled-coil domain-containing protein 89 (chains G, L)
GGGSGGGSKKHSLDLLSKERELNGKLRHLSP
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 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
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