8JE2: Neddylated Cul2-Rbx1-EloBC-FEM1B
Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B complexed with FNIP1-FLCN. Determined by electron microscopy at 3.63 Å resolution. Released 28 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 3.63 Å
- Organism
- Homo sapiens
- Chains
- 5
- Atoms
- 9,271
- Mol. weight
- 312.98 kDa
- Ligands
- ZN
- Released
- 28 Feb 2024
Explore 8JE2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8JE2 contains 65 α-helices and 10 β-strands across 5 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: 27 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-25 | 16 | |
| α-helix | 32-46 | 15 | |
| α-helix | 54-78 | 25 | |
| α-helix | 83-104 | 22 | |
| α-helix | 106-110 | 5 | |
| α-helix | 120-124 | 5 | |
| α-helix | 139-147 | 9 | |
| α-helix | 148-152 | 5 | |
| α-helix | 153-155 | 3 | |
| α-helix | 156-172 | 17 | |
| α-helix | 178-190 | 13 | |
| α-helix | 201-203 | 3 | |
| α-helix | 204-208 | 5 | |
| α-helix | 209-229 | 21 | |
| α-helix | 232-252 | 21 | |
| α-helix | 256-258 | 3 | |
| α-helix | 259-267 | 9 | |
| α-helix | 268-272 | 5 | |
| α-helix | 275-287 | 13 | |
| α-helix | 291-301 | 11 | |
| α-helix | 307-329 | 23 | |
| α-helix | 336-357 | 22 | |
| α-helix | 362-374 | 13 | |
| α-helix | 386-399 | 14 | |
| α-helix | 408-424 | 17 | |
| α-helix | 429-445 | 17 | |
| α-helix | 451-462 | 12 | |
Chain B: 3 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-9 | 5 | 1 |
| β-strand | 12-15 | 4 | 1 |
| β-strand | 23 | 1 | 2 |
| α-helix | 24-35 | 12 | |
| β-strand | 43-46 | 4 | 1 |
| β-strand | 49-50 | 2 | 1 |
| β-strand | 56 | 1 | 2 |
| β-strand | 73-78 | 6 | 1 |
| α-helix | 90-92 | 3 | |
| α-helix | 94-96 | 3 | |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-22 | 5 | 1 |
| β-strand | 28-32 | 5 | 1 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 61 | 1 | 1 |
| α-helix | 67-81 | 15 | |
| α-helix | 91-93 | 3 | |
| α-helix | 97-110 | 14 | |
Chain D: 29 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 124-131 | 8 | |
| α-helix | 134-142 | 9 | |
| α-helix | 157-164 | 8 | |
| α-helix | 167-175 | 9 | |
| α-helix | 190-196 | 7 | |
| α-helix | 200-208 | 9 | |
| α-helix | 222-228 | 7 | |
| α-helix | 232-240 | 9 | |
| α-helix | 246-262 | 17 | |
| α-helix | 269-283 | 15 | |
| α-helix | 295-298 | 4 | |
| α-helix | 311-317 | 7 | |
| α-helix | 321-337 | 17 | |
| α-helix | 344-356 | 13 | |
| α-helix | 360-377 | 18 | |
| α-helix | 382-397 | 16 | |
| α-helix | 405-428 | 24 | |
| α-helix | 430-432 | 3 | |
| α-helix | 434-456 | 23 | |
| α-helix | 461-476 | 16 | |
| α-helix | 482-484 | 3 | |
| α-helix | 487-492 | 6 | |
| α-helix | 512-520 | 9 | |
| α-helix | 535-540 | 6 | |
| α-helix | 549-560 | 12 | |
| α-helix | 576-579 | 4 | |
| α-helix | 583-592 | 10 | |
| α-helix | 597-608 | 12 | |
| α-helix | 618-626 | 9 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 575-577 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-2 | A | protein | 751 | Homo sapiens | Q13617 (AlphaFold model) |
| Elongin-B | B | protein | 104 | Homo sapiens | Q15370 (AlphaFold model) |
| Elongin-C | C | protein | 98 | Homo sapiens | Q15369 (AlphaFold model) |
| Protein fem-1 homolog B | D | protein | 630 | Homo sapiens | Q9UK73 (AlphaFold model) |
| Folliculin-interacting protein 1 | H | protein | 1172 | Homo sapiens | Q8TF40 |
Sequence of entity 1 (A), FASTA
>8JE2_1 Cullin-2 (chains A)
MSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFSDIYALCVAYPEPLGERLYTE
TKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADYMDCLYRYLNTQFIKKNKLTE
ADLQYGYGGVDMNEPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGEDPNQKV
IHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQYMEKVL
GRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMANMYVL
LRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLINTVLNG
DQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRLTSFIT
VFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHRMYTDM
SVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEKSVQMF
ELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVSYKELQ
DSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITTSMQKD
TPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSISMIKK
CIEVLIDKQYIERSQASADEYSYVAHHHHHH
Sequence of entity 2 (B), FASTA
>8JE2_2 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK
Sequence of entity 3 (C), FASTA
>8JE2_3 Elongin-C (chains C)
MAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVC
MYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 4 (D), FASTA
>8JE2_4 Protein fem-1 homolog B (chains D)
GEFMEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNG
HAKVVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHT
TVTNSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQR
ADPNAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVEL
LLSHADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLP
PIHAYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADN
MEFEQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLE
IEQSMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHL
DPRTREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALH
IIVQYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSL
KCLAARAVRANDINYQDQIPRTLEEFVGFH
Sequence of entity 5 (H), FASTA
>8JE2_5 Folliculin-interacting protein 1 (chains H)
MAPTLFQKLFSKRTGLGAPGRDARDPDCGFSWPLPEFDPSQIRLIVYQDCERRGRNVLFD
SSVKRRNEDISVSKLGSDAQVKVFGKCCQLKPGGDSSSSLDSSVTSSSDIKDQCLKYQGS
RCSSDANMLGEMMFGSVAMSYKGSTLKIHQIRSPPQLMLSKVFTARTGSSICGSLNTLQD
SLEFINQDNNTLKADNNTVINGLLGNIGLSQFCSPRRAFSEQGPLRLIRSASFFAVHSNP
MDMPGRELNEDRDSGIARSASLSSLLITPFPSPNSSLTRSCASSYQRRWRRSQTTSLENG
VFPRWSIEESFNLSDESCGPNPGIVRKKKIAIGVIFSLSKDEDENNKFNEFFFSHFPLFE
SHMNKLKSAIEQAMKMSRRSADASQRSLAYNRIVDALNEFRTTICNLYTMPRIGEPVWLT
MMSGTPEKNHLCYRFMKEFTFLMENASKNQFLPALITAVLTNHLAWVPTVMPNGQPPIKI
FLEKHSSQSVDMLAKTHPYNPLWAQLGDLYGAIGSPVRLARTVVVGKRQDMVQRLLYFLT
YFIRCSELQETHLLENGEDEAIVMPGTVITTTLEKGEIEESEYVLVTMHRNKSSLLFKES
EEIRTPNCNCKYCSHPLLGQNVENISQQEREDIQNSSKELLGISDECQMISPSDCQEENA
VDVKQYRDKLRTCFDAKLETVVCTGSVPVDKCALSESGLESTEETWQSEKLLDSDSHTGK
AMRSTGMVVEKKPPDKIVPASFSCEAAQTKVTFLIGDSMSPDSDTELRSQAVVDQITRHH
TKPLKEERGAIDQHQETKQTTKDQSGESDTQNMVSEEPCELPCWNHSDPESMSLFDEYFN
DDSIETRTIDDVPFKTSTDSKDHCCMLEFSKILCTKNNKQNNEFCKCIETVPQDSCKTCF
PQQDQRDTLSILVPHGDKESSDKKIAVGTEWDIPRNESSDSALGDSESEDTGHDMTRQVS
SYYGGEQEDWAEEDEIPFPGSKLIEVSAVQPNIANFGRSLLGGYCSSYVPDFVLQGIGSD
ERFRQCLMSDLSHAVQHPVLDEPIAEAVCIIADMDKWTVQVASSQRRVTDNKLGKEVLVS
SLVSNLLHSTLQLYKHNLSPNFCVMHLEDRLQELYFKSKMLSEYLRGQMRVHVKELGVVL
GIESSDLPLLAAVASTHSPYVAQILLENLYFQ
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Structural insights into the ubiquitylation strategy of the oligomeric CRL2 FEM1B E3 ubiquitin ligase. Dai, Z., Liang, L., Wang, W. et al. EMBO J (2024) 43:1089-1109. DOI 10.1038/s44318-024-00047-y · 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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