4F52: Glomulin-RBX1-CUL1 complex
Structure of a Glomulin-RBX1-CUL1 complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 19 Sept 2012.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 13,897
- Mol. weight
- 226.36 kDa
- Ligands
- ZN
- Released
- 19 Sept 2012
Explore 4F52 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4F52 contains 98 α-helices and 39 β-strands across 6 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: 11 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 421-430 | 10 | |
| α-helix | 443-454 | 12 | |
| α-helix | 459-475 | 17 | |
| α-helix | 482-496 | 15 | |
| α-helix | 498-525 | 28 | |
| α-helix | 529-531 | 3 | |
| β-strand | 534-541 | 8 | 1 |
| α-helix | 557-573 | 17 | |
| β-strand | 577-592 | 16 | 1 |
| β-strand | 600-604 | 5 | 1 |
| α-helix | 605-611 | 7 | |
| α-helix | 612-615 | 4 | |
| β-strand | 619-621 | 3 | 2 |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
| β-strand | 649-650 | 2 | 2 |
| β-strand | 668-671 | 4 | 2 |
| β-strand | 679 | 1 | 3 |
| β-strand | 681-683 | 3 | 1 |
Chain B: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-35 | 14 | 1 |
| α-helix | 36-37 | 2 | |
| β-strand | 41 | 1 | 4 |
| β-strand | 48 | 1 | 4 |
| α-helix | 54-57 | 4 | |
| α-helix | 60 | 1 | |
| β-strand | 70-72 | 3 | 5 |
| β-strand | 73 | 1 | 6 |
| β-strand | 78-80 | 3 | 5 |
| α-helix | 81-87 | 7 | |
| β-strand | 93 | 1 | 7 |
| β-strand | 100 | 1 | 7 |
| β-strand | 103 | 1 | 6 |
Chain C: 12 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 420-428 | 9 | |
| α-helix | 446-454 | 9 | |
| α-helix | 463-475 | 13 | |
| α-helix | 483-492 | 10 | |
| α-helix | 498-526 | 29 | |
| β-strand | 534-541 | 8 | 8 |
| α-helix | 549-552 | 4 | |
| α-helix | 557-573 | 17 | |
| β-strand | 578-581 | 4 | 8 |
| α-helix | 583-585 | 3 | |
| β-strand | 587-592 | 6 | 8 |
| β-strand | 600-604 | 5 | 8 |
| α-helix | 605-612 | 8 | |
| α-helix | 613-615 | 3 | |
| β-strand | 619-621 | 3 | 9 |
| α-helix | 622-629 | 8 | |
| α-helix | 633-645 | 13 | |
| β-strand | 649-651 | 3 | 9 |
| β-strand | 656 | 1 | 3 |
| β-strand | 668-671 | 4 | 9 |
| β-strand | 681-683 | 3 | 8 |
Chain D: 4 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-34 | 13 | 8 |
| α-helix | 35-37 | 3 | |
| β-strand | 41 | 1 | 10 |
| β-strand | 48 | 1 | 10 |
| α-helix | 54-58 | 5 | |
| β-strand | 70-72 | 3 | 11 |
| β-strand | 73 | 1 | 12 |
| β-strand | 78-80 | 3 | 11 |
| α-helix | 81-90 | 10 | |
| β-strand | 93 | 1 | 13 |
| β-strand | 100 | 1 | 13 |
| α-helix | 101 | 1 | |
| β-strand | 103 | 1 | 12 |
Chain E: 37 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-13 | 12 | |
| α-helix | 28-37 | 10 | |
| α-helix | 43-49 | 7 | |
| α-helix | 55-60 | 6 | |
| α-helix | 62-65 | 4 | |
| α-helix | 66-74 | 9 | |
| α-helix | 84-96 | 13 | |
| α-helix | 99-101 | 3 | |
| α-helix | 102-106 | 5 | |
| α-helix | 107-110 | 4 | |
| α-helix | 115-117 | 3 | |
| α-helix | 118-135 | 18 | |
| α-helix | 140-156 | 17 | |
| α-helix | 158-160 | 3 | |
| α-helix | 173-192 | 20 | |
| α-helix | 199-222 | 24 | |
| α-helix | 236-250 | 15 | |
| α-helix | 255-257 | 3 | |
| α-helix | 283-290 | 8 | |
| α-helix | 291-295 | 5 | |
| α-helix | 309-324 | 16 | |
| α-helix | 329-344 | 16 | |
| α-helix | 347 | 1 | |
| β-strand | 351 | 1 | 14 |
| α-helix | 353-357 | 5 | |
| α-helix | 359-374 | 16 | |
| α-helix | 378-394 | 17 | |
| β-strand | 395 | 1 | 14 |
| α-helix | 397-411 | 15 | |
| α-helix | 414-430 | 17 | |
| α-helix | 444-453 | 10 | |
| α-helix | 468-484 | 17 | |
| α-helix | 486 | 1 | |
| α-helix | 494-496 | 3 | |
| α-helix | 498-501 | 4 | |
| α-helix | 502-506 | 5 | |
| α-helix | 507-533 | 27 | |
| α-helix | 553-555 | 3 | |
| α-helix | 556-581 | 26 | |
Chain F: 30 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-14 | 13 | |
| α-helix | 24-37 | 14 | |
| α-helix | 55-60 | 6 | |
| α-helix | 63-65 | 3 | |
| α-helix | 66-73 | 8 | |
| α-helix | 84-95 | 12 | |
| α-helix | 99-107 | 9 | |
| α-helix | 108-110 | 3 | |
| α-helix | 117-135 | 19 | |
| α-helix | 141-154 | 14 | |
| α-helix | 158-159 | 2 | |
| α-helix | 173-192 | 20 | |
| α-helix | 202-222 | 21 | |
| α-helix | 236-250 | 15 | |
| α-helix | 283-294 | 12 | |
| α-helix | 300-302 | 3 | |
| α-helix | 309-324 | 16 | |
| α-helix | 329-343 | 15 | |
| α-helix | 347 | 1 | |
| β-strand | 351 | 1 | 15 |
| α-helix | 353-357 | 5 | |
| α-helix | 359-374 | 16 | |
| α-helix | 378-394 | 17 | |
| β-strand | 395 | 1 | 15 |
| α-helix | 397-410 | 14 | |
| α-helix | 414-429 | 16 | |
| α-helix | 444-453 | 10 | |
| α-helix | 468-484 | 17 | |
| α-helix | 498-501 | 4 | |
| α-helix | 502-506 | 5 | |
| α-helix | 507-529 | 23 | |
| α-helix | 551-582 | 32 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cullin-1 | A, C | protein | 282 | Homo sapiens | Q13616 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1 | B, D | protein | 106 | Homo sapiens | P62877 (AlphaFold model) |
| Glomulin | E, F | protein | 596 | Homo sapiens | Q92990 (AlphaFold model) |
Sequence of entity 1 (A, C), FASTA
>4F52_1 Cullin-1 (chains A, C)
GSMAQSSSKSPEELARYCDSLLKKSSKNPEEAELEDTLNQVMEKFKKIEDKDVFQKFYAK
MLAKRLVHQNSASDDAEASMISKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNS
EPLDLDFSIQVLSSGSWPFQQSCTFALPSELERSYQRFTAFYASRHSGRKLTWLYQLSKG
ELVTNCFKNRYTLQASTFQMAILLQYNTEDAYTVQQLTDSTQIKMDILAQVLQILLKSKL
LVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKT
Sequence of entity 2 (B, D), FASTA
>4F52_2 E3 ubiquitin-protein ligase RBX1 (chains B, D)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
Sequence of entity 3 (E, F), FASTA
>4F52_3 Glomulin (chains E, F)
GSMAVEELQSIIKRCQILEEQDFKEEDFGLFQLAGQRCIEEGHTDQLLEIIQNEKNKVII
KNMGWNLVGPVVRCLLCKDKEDSKRKVYFLIFDLLVKLCNPKELLLGLLELIEEPSGKQI
SQSILLLLQPLQTVIQKLHNKAYSIGLALSTLWNQLSLLPVPYSKEQIQMDDYGLCQCCK
ALIEFTKPFVEEVIDNKENSLENEKLKDELLKFCFKSLKCPLLTAQFFEQSEEGGNDPFR
YFASEIIGFLSAIGHPFPKMIFNHGRKKRTWNYLEFEEEENKQLADSMASLAYLVFVQGI
HIDQLPMVLSPLYLLQFNMGHIEVFLQRTEESVISKGLELLENSLLRIEDNSLLYQYLEI
KSFLTVPQGLVKVMTLCPIETLRKKSLAMLQLYINKLDSQGKYTLFRCLLNTSNHSGVEA
FIIQNIKNQIDMSLKRTRNNKWFTGPQLISLLDLVLFLPEGAETDLLQNSDRIMASLNLL
RYLVIKDNENDNQTGLWTELGNIENNFLKPLHIGLNMSKAHYEAEIKNSQEAQKSKDLCS
ITVSGEEIPNMPPEMQLKVLHSALFTFDLIESVLARVEELIEIKTKSTSEENIGIK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 6 |
Primary citation
Structure of a Glomulin-RBX1-CUL1 Complex: Inhibition of a RING E3 Ligase through Masking of Its E2-Binding Surface. Duda, D.M., Olszewski, J.L., Tron, A.E. et al. Mol Cell (2012) 47:371-382. DOI 10.1016/j.molcel.2012.05.044 · PubMed
Other PDB entries of the same protein (UniProt Q13616 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
- 5V89 1.55 Å, Structure of DCN4 PONY domain bound to CUL1 WHB
- 3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
- 8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
- 7Z8R 2.7 Å, CAND1-CUL1-RBX1
- 7Z8V 2.7 Å, CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked
- 8OR3 2.9 Å, CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1
- 9QO4 2.95 Å, Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex
- 1LDJ 3.0 Å, Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex
- 7Z8T 3.0 Å, CAND1-SCF-SKP2 CAND1 engaged SCF rocked
- 9XZL 3.0 Å, Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex…
- 9EFV 3.03 Å, Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3
Browse structure collections
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