9J79: CRL2-FEM1B
Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer). Determined by electron microscopy at 4.08 Å resolution. Released 9 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 4.08 Å
- Organism
- Homo sapiens
- Chains
- 19
- Atoms
- 36,721
- Mol. weight
- 584.62 kDa
- Ligands
- ZN
- Released
- 9 Apr 2025
Explore 9J79 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9J79 contains 252 α-helices and 85 β-strands across 19 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: 34 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 18-23 | 6 | |
| α-helix | 29-36 | 8 | |
| β-strand | 41-42 | 2 | 27 |
| β-strand | 45-46 | 2 | 27 |
| α-helix | 49-56 | 8 | |
| α-helix | 59-67 | 9 | |
| α-helix | 91-98 | 8 | |
| α-helix | 101-110 | 10 | |
| α-helix | 124-131 | 8 | |
| α-helix | 134-142 | 9 | |
| β-strand | 150 | 1 | 28 |
| β-strand | 156 | 1 | 28 |
| α-helix | 157-163 | 7 | |
| α-helix | 167-175 | 9 | |
| α-helix | 200-208 | 9 | |
| α-helix | 222-228 | 7 | |
| α-helix | 232-239 | 8 | |
| α-helix | 246-261 | 16 | |
| α-helix | 269-283 | 15 | |
| α-helix | 300-302 | 3 | |
| α-helix | 311-316 | 6 | |
| α-helix | 321-336 | 16 | |
| α-helix | 341-343 | 3 | |
| α-helix | 344-356 | 13 | |
| α-helix | 360-377 | 18 | |
| α-helix | 382-397 | 16 | |
| α-helix | 404-427 | 24 | |
| α-helix | 433-456 | 24 | |
| α-helix | 461-477 | 17 | |
| α-helix | 487-492 | 6 | |
| α-helix | 503-506 | 4 | |
| α-helix | 512-521 | 10 | |
| α-helix | 535-540 | 6 | |
| α-helix | 549-559 | 11 | |
| β-strand | 570 | 1 | 29 |
| β-strand | 574 | 1 | 29 |
| α-helix | 583-592 | 10 | |
| α-helix | 600-607 | 8 | |
| α-helix | 618-626 | 9 | |
Chain B: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 68-83 | 16 | |
| α-helix | 86-99 | 14 | |
| α-helix | 106-110 | 5 | |
| α-helix | 116-123 | 8 | |
Chain C: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 42-57 | 16 | |
| α-helix | 61-74 | 14 | |
| α-helix | 78-87 | 10 | |
| α-helix | 91-100 | 10 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-9 | 8 | |
Chain E: 39 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-25 | 16 | |
| α-helix | 32-44 | 13 | |
| α-helix | 54-78 | 25 | |
| α-helix | 83-104 | 22 | |
| α-helix | 106-108 | 3 | |
| α-helix | 109-113 | 5 | |
| α-helix | 139-147 | 9 | |
| α-helix | 148-152 | 5 | |
| α-helix | 153-155 | 3 | |
| α-helix | 156-171 | 16 | |
| α-helix | 178-190 | 13 | |
| α-helix | 191-194 | 4 | |
| α-helix | 201-203 | 3 | |
| α-helix | 204-208 | 5 | |
| α-helix | 209-226 | 18 | |
| α-helix | 232-253 | 22 | |
| α-helix | 256-258 | 3 | |
| α-helix | 259-270 | 12 | |
| α-helix | 275-288 | 14 | |
| α-helix | 291-303 | 13 | |
| α-helix | 308-326 | 19 | |
| α-helix | 335-356 | 22 | |
| α-helix | 362-376 | 15 | |
| α-helix | 379-380 | 2 | |
| α-helix | 387-399 | 13 | |
| β-strand | 400 | 1 | 1 |
| α-helix | 408-422 | 15 | |
| α-helix | 428-445 | 18 | |
| β-strand | 448 | 1 | 1 |
| α-helix | 451-465 | 15 | |
| α-helix | 471-491 | 21 | |
| α-helix | 493-496 | 4 | |
| β-strand | 510-512 | 3 | 2 |
| α-helix | 527-530 | 4 | |
| α-helix | 534-547 | 14 | |
| β-strand | 552-553 | 2 | 3 |
| β-strand | 556-561 | 6 | 2 |
| β-strand | 564 | 1 | 4 |
| β-strand | 575 | 1 | 4 |
| α-helix | 579-586 | 8 | |
| α-helix | 587-589 | 3 | |
| β-strand | 593-594 | 2 | 5 |
| α-helix | 596-603 | 8 | |
| α-helix | 607-618 | 12 | |
| β-strand | 638-639 | 2 | 5 |
| α-helix | 662-691 | 30 | |
| β-strand | 693-694 | 2 | 6 |
| α-helix | 696-707 | 12 | |
| α-helix | 715-727 | 13 | |
| β-strand | 731-733 | 3 | 6 |
| β-strand | 741-743 | 3 | 6 |
Chain F: 5 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 18-19 | 2 | 7 |
| β-strand | 21-22 | 2 | 8 |
| β-strand | 28 | 1 | 8 |
| β-strand | 31-32 | 2 | 7 |
| α-helix | 33-36 | 4 | |
| α-helix | 40-46 | 7 | |
| β-strand | 60-61 | 2 | 8 |
| α-helix | 67-82 | 16 | |
| α-helix | 91-94 | 4 | |
| α-helix | 103-110 | 8 | |
Chain G: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 65-83 | 19 | |
| α-helix | 86-98 | 13 | |
| α-helix | 103-113 | 11 | |
| α-helix | 116-125 | 10 | |
Chain H: 4 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-4 | 2 | 9 |
| β-strand | 6-8 | 3 | 10 |
| β-strand | 12 | 1 | 8 |
| β-strand | 13-14 | 2 | 10 |
| β-strand | 17-18 | 2 | 9 |
| α-helix | 24-35 | 12 | |
| α-helix | 58-60 | 3 | |
| β-strand | 68 | 1 | 11 |
| β-strand | 71 | 1 | 11 |
| α-helix | 72-73 | 2 | |
| β-strand | 74-75 | 2 | 10 |
| α-helix | 91-99 | 9 | |
11 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 | E, K | protein | 750 | Homo sapiens | Q13617 (AlphaFold model) |
| Elongin-C | F, L | protein | 96 | Homo sapiens | Q15369 (AlphaFold model) |
| Elongin-B | H, M | protein | 121 | Homo sapiens | Q15370 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1, N-terminally processed | I, N | protein | 96 | Homo sapiens | P62877 (AlphaFold model) |
| Protein fem-1 homolog B | A, J, O, P | protein | 627 | Homo sapiens | Q9UK73 |
| Mitochondrial import receptor subunit TOM20 homolog | B, C, G, S | protein | 121 | Homo sapiens | Q15388 |
| Poly-UNK | D, R | protein | 10 | Homo sapiens | |
| Poly-UNK | Q | protein | 8 | Homo sapiens | |
Sequence of entity 1 (E, K), FASTA
>9J79_1 Cullin-2 (chains E, K)
SASWSHPQFEKGGGSGGGSGTSLKPRVVDFDETWNKLLTTIKAVVMLEYVERATWNDRFS
DIYALCVAYPEPLGERLYTETKIFLENHVRHLHKRVLESEEQVLVMYHRYWEEYSKGADY
MDCLYRYLNTQFIKKNGGGPLMEIGELALDMWRKLMVEPLQAILIRMLLREIKNDRGGED
PNQKVIHGVINSFVHVEQYKKKFPLKFYQEIFESPFLTETGEYYKQEASNLLQESNCSQY
MEKVLGRLKDEEIRCRKYLHPSSYTKVIHECQQRMVADHLQFLHAECHNIIRQEKKNDMA
NMYVLLRAVSTGLPHMIQELQNHIHDEGLRATSNLTQENMPTLFVESVLEVHGKFVQLIN
TVLNGDQHFMSALDKALTSVVNYREPKSVCKAPELLAKYCDNLLKKSAKGMTENEVEDRL
TSFITVFKYIDDKDVFQKFYARMLAKRLIHGLSMSMDSEEAMINKLKQACGYEFTSKLHR
MYTDMSVSADLNNKFNNFIKNQDTVIDLGISFQIYVLQAGAWPLTQAPSSTFAIPQELEK
SVQMFELFYSQHFSGRKLTWLHYLCTGEVKMNYLGKPYVAMVTTYQMAVLLAFNNSETVS
YKELQDSTQMNEKELTKTIKSLLDVKMINHDSEKEDIDAESSFSLNMNFSSKRTKFKITT
SMQKDTPQEMEQTRSAVDEDRKMYLQAAIVRIMKARKVLRHNALIQEVISQSRARFNPSI
SMIKKCIEVLIDKQYIERSQASADEYSYVA
Sequence of entity 2 (F, L), FASTA
>9J79_2 Elongin-C (chains F, L)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC
Sequence of entity 3 (H, M), FASTA
>9J79_3 Elongin-B (chains H, M)
GGSMDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTL
GECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAV
Q
Sequence of entity 4 (I, N), FASTA
>9J79_4 E3 ubiquitin-protein ligase RBX1, N-terminally processed (chains I, N)
SHMGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAW
GVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 5 (A, J, O, P), FASTA
>9J79_5 Protein fem-1 homolog B (chains A, J, O, P)
MEGLAGYVYKAASEGKVLTLAALLLNRSESDIRYLLGYVSQQGGQRSTPLIIAARNGHAK
VVRLLLEHYRVQTQQTGTVRFDGYVIDGATALWCAAGAGHFEVVKLLVSHGANVNHTTVT
NSTPLRAACFDGRLDIVKYLVENNANISIANKYDNTCLMIAAYKGHTDVVRYLLEQRADP
NAKAHCGATALHFAAEAGHIDIVKELIKWRAAIVVNGHGMTPLKVAAESCKADVVELLLS
HADCDRRSRIEALELLGASFANDRENYDIIKTYHYLYLAMLERFQDGDNILEKEVLPPIH
AYGNRTECRNPQELESIRQDRDALHMEGLIVRERILGADNIDVSHPIIYRGAVYADNMEF
EQCIKLWLHALHLRQKGNRNTHKDLLRFAQVFSQMIHLNETVKAPDIECVLRCSVLEIEQ
SMNRVKNISDADVHNAMDNYECNLYTFLYLVCISTKTQCSEEDQCKINKQIYNLIHLDPR
TREGFTLLHLAVNSNTPVDDFHTNDVCSFPNALVTKLLLDCGAEVNAVDNEGNSALHIIV
QYNRPISDFLTLHSIIISLVEAGAHTDMTNKQNKTPLDKSTTGVSEILLKTQMKMSLKCL
AARAVRANDINYQDQIPRTLEEFVGFH
Sequence of entity 6 (B, C, G, S), FASTA
>9J79_6 Mitochondrial import receptor subunit TOM20 homolog (chains B, C, G, S)
DRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFFLEEIQLGEELLAQG
EYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLAEDDV
E
Sequence of entity 7 (D, R), FASTA
>9J79_7 Poly-UNK (chains D, R)
XXXXXXXXXX
Sequence of entity 8 (Q), FASTA
>9J79_8 Poly-UNK (chains Q)
XXXXXXXX
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 6 |
Primary citation
TOM20-driven E3 ligase recruitment regulates mitochondrial dynamics through PLD6. Raiff, A., Zhao, S., Bekturova, A. et al. Nat Chem Biol (2026) 22:37-47. DOI 10.1038/s41589-025-01894-4 · 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…
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