8GQ6: KBTBD2-CUL3-Rbx1 dimeric complex
Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex. Determined by electron microscopy at 3.96 Å resolution. Released 6 Sept 2023.
- Method
- Electron microscopy
- Resolution
- 3.96 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 22,293
- Mol. weight
- 351.35 kDa
- Ligands
- ZN
- Released
- 6 Sept 2023
Explore 8GQ6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8GQ6 contains 112 α-helices and 92 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: 19 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-27 | 15 | |
| β-strand | 33-37 | 5 | 1 |
| β-strand | 40-44 | 5 | 1 |
| α-helix | 46-52 | 7 | |
| α-helix | 56-61 | 6 | |
| β-strand | 71-73 | 3 | 1 |
| α-helix | 79-91 | 13 | |
| α-helix | 101-111 | 11 | |
| α-helix | 114-125 | 12 | |
| α-helix | 132-142 | 11 | |
| α-helix | 146-163 | 18 | |
| α-helix | 167-170 | 4 | |
| α-helix | 174-182 | 9 | |
| α-helix | 192-203 | 12 | |
| α-helix | 210-220 | 11 | |
| α-helix | 222-225 | 4 | |
| α-helix | 229-236 | 8 | |
| α-helix | 237-238 | 2 | |
| α-helix | 243-249 | 7 | |
| β-strand | 266-275 | 10 | 2 |
| β-strand | 283-288 | 6 | 2 |
| β-strand | 295-298 | 4 | 2 |
| β-strand | 306 | 1 | 3 |
| β-strand | 309-312 | 4 | 4 |
| β-strand | 318-321 | 4 | 4 |
| β-strand | 324-325 | 2 | 3 |
| β-strand | 345-346 | 2 | 3 |
| β-strand | 350-353 | 4 | 4 |
| β-strand | 360-362 | 3 | 4 |
| β-strand | 374-378 | 5 | 5 |
| β-strand | 381-385 | 5 | 5 |
| β-strand | 399-403 | 5 | 5 |
| β-strand | 408-411 | 4 | 5 |
| α-helix | 413-415 | 3 | |
| β-strand | 423-427 | 5 | 6 |
| β-strand | 430-434 | 5 | 6 |
| β-strand | 439-443 | 5 | 6 |
| β-strand | 448-451 | 4 | 6 |
| β-strand | 463-467 | 5 | 7 |
| β-strand | 470-474 | 5 | 7 |
| β-strand | 499-503 | 5 | 7 |
| β-strand | 508-511 | 4 | 7 |
| β-strand | 524 | 1 | 8 |
| β-strand | 527-530 | 4 | 8 |
| β-strand | 533-540 | 8 | 8 |
| β-strand | 548-555 | 8 | 8 |
| β-strand | 560-567 | 8 | 8 |
| α-helix | 568 | 1 | |
| β-strand | 580-586 | 7 | 2 |
| β-strand | 592-593 | 2 | 2 |
| α-helix | 594-595 | 2 | |
Chain B: 18 helices, 32 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-27 | 17 | |
| β-strand | 33-37 | 5 | 14 |
| β-strand | 40-44 | 5 | 14 |
| α-helix | 46-52 | 7 | |
| α-helix | 57-60 | 4 | |
| β-strand | 71-73 | 3 | 14 |
| α-helix | 79-91 | 13 | |
| α-helix | 101-111 | 11 | |
| α-helix | 114-127 | 14 | |
| α-helix | 133-142 | 10 | |
| α-helix | 146-163 | 18 | |
| α-helix | 167-169 | 3 | |
| α-helix | 174-182 | 9 | |
| α-helix | 192-202 | 11 | |
| α-helix | 210-216 | 7 | |
| α-helix | 231-235 | 5 | |
| α-helix | 238 | 1 | |
| α-helix | 245-249 | 5 | |
| β-strand | 266-275 | 10 | 15 |
| α-helix | 276 | 1 | |
| β-strand | 283-288 | 6 | 15 |
| β-strand | 295-298 | 4 | 15 |
| α-helix | 299-301 | 3 | |
| β-strand | 306 | 1 | 16 |
| β-strand | 309-312 | 4 | 17 |
| β-strand | 318-321 | 4 | 17 |
| β-strand | 324-325 | 2 | 16 |
| β-strand | 345-346 | 2 | 16 |
| β-strand | 350-353 | 4 | 17 |
| β-strand | 360-362 | 3 | 17 |
| β-strand | 374-378 | 5 | 18 |
| β-strand | 381-385 | 5 | 18 |
| β-strand | 400-403 | 4 | 18 |
| β-strand | 408-411 | 4 | 18 |
| α-helix | 413-415 | 3 | |
| β-strand | 423-427 | 5 | 19 |
| β-strand | 430-434 | 5 | 19 |
| β-strand | 439-443 | 5 | 19 |
| β-strand | 448-451 | 4 | 19 |
| β-strand | 463-467 | 5 | 20 |
| β-strand | 470-474 | 5 | 20 |
| β-strand | 498-503 | 6 | 20 |
| β-strand | 508-514 | 7 | 20 |
| β-strand | 524 | 1 | 21 |
| β-strand | 527-530 | 4 | 21 |
| β-strand | 533-541 | 9 | 21 |
| β-strand | 547-555 | 9 | 21 |
| β-strand | 560-566 | 7 | 21 |
| β-strand | 580-586 | 7 | 15 |
| β-strand | 593 | 1 | 15 |
Chain C: 36 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-45 | 19 | |
| α-helix | 55-66 | 12 | |
| α-helix | 70-84 | 15 | |
| α-helix | 85-89 | 5 | |
| α-helix | 90-95 | 6 | |
| α-helix | 101-133 | 33 | |
| α-helix | 139-147 | 9 | |
| α-helix | 148-152 | 5 | |
| α-helix | 157-174 | 18 | |
| α-helix | 181-194 | 14 | |
| α-helix | 200-201 | 2 | |
| α-helix | 202-206 | 5 | |
| α-helix | 207-227 | 21 | |
| α-helix | 233-251 | 19 | |
| α-helix | 258-272 | 15 | |
| α-helix | 285-289 | 5 | |
| α-helix | 293-303 | 11 | |
| α-helix | 309-328 | 20 | |
| α-helix | 338-355 | 18 | |
| α-helix | 356-360 | 5 | |
| α-helix | 364-378 | 15 | |
| α-helix | 384-397 | 14 | |
| α-helix | 405-420 | 16 | |
| α-helix | 425-440 | 16 | |
| α-helix | 450-461 | 12 | |
| α-helix | 467-494 | 28 | |
| β-strand | 502-503 | 2 | 9 |
| β-strand | 506-509 | 4 | 10 |
| α-helix | 523-525 | 3 | |
| α-helix | 526-541 | 16 | |
| β-strand | 546-549 | 4 | 10 |
| β-strand | 557-561 | 5 | 9 |
| β-strand | 591-594 | 4 | 9 |
| α-helix | 599-607 | 9 | |
| α-helix | 613-618 | 6 | |
| α-helix | 625-634 | 10 | |
| β-strand | 645-646 | 2 | 13 |
| β-strand | 659-660 | 2 | 13 |
| β-strand | 671 | 1 | 9 |
| α-helix | 685-710 | 26 | |
| α-helix | 711-713 | 3 | |
| α-helix | 722-729 | 8 | |
| α-helix | 738-745 | 8 | |
| α-helix | 748-750 | 3 | |
Chain D: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-27 | 6 | 22 |
| β-strand | 30-34 | 5 | 23 |
| β-strand | 70-72 | 3 | 25 |
| β-strand | 78-80 | 3 | 25 |
| α-helix | 81-85 | 5 | |
| α-helix | 100-101 | 2 | |
| β-strand | 105-106 | 2 | 25 |
Chain E: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 22-27 | 6 | 9 |
| β-strand | 30-35 | 6 | 10 |
| β-strand | 70-72 | 3 | 11 |
| β-strand | 78-80 | 3 | 11 |
| α-helix | 81-87 | 7 | |
| β-strand | 93 | 1 | 12 |
| β-strand | 100 | 1 | 12 |
| α-helix | 101 | 1 | |
| β-strand | 105-106 | 2 | 11 |
Chain F: 35 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-45 | 19 | |
| α-helix | 55-66 | 12 | |
| α-helix | 70-84 | 15 | |
| α-helix | 85-89 | 5 | |
| α-helix | 90-95 | 6 | |
| α-helix | 101-133 | 33 | |
| α-helix | 139-147 | 9 | |
| α-helix | 148-152 | 5 | |
| α-helix | 157-174 | 18 | |
| α-helix | 181-194 | 14 | |
| α-helix | 200-201 | 2 | |
| α-helix | 202-206 | 5 | |
| α-helix | 207-227 | 21 | |
| α-helix | 233-251 | 19 | |
| α-helix | 258-272 | 15 | |
| α-helix | 285-289 | 5 | |
| α-helix | 293-303 | 11 | |
| α-helix | 309-328 | 20 | |
| α-helix | 338-355 | 18 | |
| α-helix | 356-360 | 5 | |
| α-helix | 364-378 | 15 | |
| α-helix | 384-397 | 14 | |
| α-helix | 405-420 | 16 | |
| α-helix | 425-440 | 16 | |
| α-helix | 450-461 | 12 | |
| α-helix | 467-494 | 28 | |
| β-strand | 502-503 | 2 | 22 |
| β-strand | 506-509 | 4 | 23 |
| α-helix | 526-541 | 16 | |
| β-strand | 547-549 | 3 | 23 |
| β-strand | 557-561 | 5 | 22 |
| β-strand | 591-594 | 4 | 22 |
| α-helix | 599-607 | 9 | |
| α-helix | 615-618 | 4 | |
| α-helix | 625-634 | 10 | |
| β-strand | 645-646 | 2 | 24 |
| β-strand | 659-660 | 2 | 24 |
| β-strand | 671 | 1 | 22 |
| α-helix | 685-710 | 26 | |
| α-helix | 711-713 | 3 | |
| α-helix | 722-729 | 8 | |
| α-helix | 738-745 | 8 | |
| α-helix | 748-750 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Kelch repeat and BTB domain-containing protein 2 | A, B | protein | 623 | Homo sapiens | Q8IY47 (AlphaFold model) |
| E3 ubiquitin-protein ligase RBX1 | D, E | protein | 121 | Homo sapiens | P62877 (AlphaFold model) |
| Cullin-3 | C, F | protein | 776 | Homo sapiens | Q13618 (AlphaFold model) |
Sequence of entity 1 (A, B), FASTA
>8GQ6_1 Kelch repeat and BTB domain-containing protein 2 (chains A, B)
MSTQDERQINTEYAVSLLEQLKLFYEQQLFTDIVLIVEGTEFPCHKMVLATCSSYFRAMF
MSGLSESKQTHVHLRNVDAATLQIIITYAYTGNLAMNDSTVEQLYETACFLQVEDVLQRC
REYLIKKINAENCVRLLSFADLFSCEELKQSAKRMVEHKFTAVYHQDAFMQLSHDLLIDI
LSSDNLNVEKEETVREAAMLWLEYNTESRSQYLSSVLSQIRIDALSEVTQRAWFQGLPPN
DKSVVVQGLYKSMPKFFKPRLGMTKEEMMIFIEASSENPCSLYSSVCYSPQAEKVYKLCS
PPADLHKVGTVVTPDNDIYIAGGQVPLKNTKTNHSKTSKLQTAFRTVNCFYWFDAQQNTW
FPKTPMLFVRIKPSLVCCEGYIYAIGGDSVGGELNRRTVERYDTEKDEWTMVSPLPCAWQ
WSAAVVVHDCIYVMTLNLMYCYFPRSDSWVEMAMRQTSRSFASAAAFGDKIFYIGGLHIA
TNSGIRLPSGTVDGSSVTVEIYDVNKNEWKMAANIPAKRYSDPCVRAVVISNSLCVFMRE
THLNERAKYVTYQYDLELDRWSLRQHISERVLWDLGRDFRCTVGKLYPSCLEESPWKPPT
YLFSTDGTEEFELDGEMVALPPV
Sequence of entity 2 (D, E), FASTA
>8GQ6_2 E3 ubiquitin-protein ligase RBX1 (chains D, E)
HHHHHHENLYFQGMAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRN
HIMDLCIECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYG
H
Sequence of entity 3 (C, F), FASTA
>8GQ6_3 Cullin-3 (chains C, F)
WSHPQFEKMSNLSKGTGSRKDTKMRIRAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGL
SFEELYRNAYTMVLHKHGEKLYTGLREVVTEHLINKVREDVLNSLNNNFLQTLNQAWNDH
QTAMVMIRDILMYMDRVYVQQNNVENVYNLGLIIFRDQVVRYGCIRDHLRQTLLDMIARE
RKGEVVDRGAIRNACQMLMILGLEGRSVYEEDFEAPFLEMSAEFFQMESQKFLAENSASV
YIKKVEARINEEIERVMHCLDKSTEEPIVKVVERELISKHMKTIVEMENSGLVHMLKNGK
TEDLGCMYKLFSRVPNGLKTMCECMSSYLREQGKALVSEEGEGKNPVDYIQGLLDLKSRF
DRFLLESFNNDRLFKQTIAGDFEYFLNLNSRSPEYLSLFIDDKLKKGVKGLTEQEVETIL
DKAMVLFRFMQEKDVFERYYKQHLARRLLTNKSVSDDSEKNMISKLKTECGCQFTSKLEG
MFRDMSISNTTMDEFRQHLQATGVSLGGVDLTVRVLTTGYWPTQSATPKCNIPPAPRHAF
EIFRRFYLAKHSGRQLTLQHHMGSADLNATFYGPVKKEDGSEVGVGGAQVTGSNTRKHIL
QVSTFQMTILMLFNNREKYTFEEIQQETDIPERELVRALQSLACGKPTQRVLTKEPKSKE
IENGHIFTVNDQFTSKLHRVKIQTVAAKQGESDPERKETRQKVDDDRKHEIEAAIVRIMK
SRKKMQHNVLVAEVTQQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 6 |
Primary citation
Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3 KBTBD2. Hu, Y., Zhang, Z., Mao, Q. et al. Nat Struct Mol Biol (2024) 31:336-350. DOI 10.1038/s41594-023-01182-6 · PubMed
Other PDB entries of the same protein (UniProt Q8IY47 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8H38 4.25 Å, Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex
- 8H36 4.6 Å, Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex
- 8H3R 6.36 Å, Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex
- 8H3F 6.73 Å, Cryo-EM Structure of the KBTBD2-CRL3-CSN complex
- 8H35 7.41 Å, Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex
- 8H3A 7.51 Å, Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex
- 8H37 7.52 Å, Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex
- 8H33 7.86 Å, Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex
- 8H34 7.99 Å, Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex
Browse structure collections
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