6AQR: SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73
SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Jul 2018.
- Method
- X-ray diffraction
- Resolution
- 2.1 Å
- Organisms
- Saccharomyces cerevisiae S288c, Homo sapiens
- Chains
- 5
- Atoms
- 6,575
- Mol. weight
- 96.32 kDa
- Ligands
- ZN
- Released
- 4 Jul 2018
Explore 6AQR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6AQR contains 42 α-helices and 45 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: 22 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| α-helix | 14-32 | 19 | |
| α-helix | 36-43 | 8 | |
| β-strand | 45 | 1 | 1 |
| β-strand | 52 | 1 | 1 |
| β-strand | 57-60 | 4 | 2 |
| β-strand | 66-68 | 3 | 2 |
| α-helix | 73-81 | 9 | |
| β-strand | 85-88 | 4 | 2 |
| β-strand | 94-96 | 3 | 2 |
| β-strand | 101-102 | 2 | 2 |
| α-helix | 107-110 | 4 | |
| α-helix | 112-117 | 6 | |
| α-helix | 118-124 | 7 | |
| β-strand | 125-126 | 2 | 3 |
| α-helix | 127-129 | 3 | |
| α-helix | 130-132 | 3 | |
| α-helix | 146-156 | 11 | |
| α-helix | 159-166 | 8 | |
| α-helix | 169-173 | 5 | |
| α-helix | 183-195 | 13 | |
| α-helix | 214-226 | 13 | |
| α-helix | 228-230 | 3 | |
| β-strand | 236-237 | 2 | 4 |
| α-helix | 238-256 | 19 | |
| β-strand | 281-288 | 8 | 5 |
| β-strand | 298-303 | 6 | 5 |
| β-strand | 306-309 | 4 | 6 |
| β-strand | 315 | 1 | 7 |
| α-helix | 316-324 | 9 | |
| β-strand | 327-328 | 2 | 5 |
| α-helix | 344-345 | 2 | |
| β-strand | 346-353 | 8 | 5 |
| β-strand | 354 | 1 | 8 |
| β-strand | 357-363 | 7 | 6 |
| β-strand | 365-368 | 4 | 9 |
| β-strand | 372-375 | 4 | 9 |
| β-strand | 381 | 1 | 7 |
| β-strand | 385-387 | 3 | 6 |
| α-helix | 389-391 | 3 | |
| β-strand | 392 | 1 | 5 |
| α-helix | 406-408 | 3 | |
| β-strand | 409-421 | 13 | 6 |
| β-strand | 426-433 | 8 | 6 |
| α-helix | 435-437 | 3 | |
| β-strand | 439-443 | 5 | 6 |
| β-strand | 446-450 | 5 | 6 |
| α-helix | 452-455 | 4 | |
| β-strand | 460-470 | 11 | 6 |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-18 | 13 | |
| α-helix | 21-35 | 15 | |
| α-helix | 38-53 | 16 | |
| α-helix | 58-71 | 14 | |
| α-helix | 75-90 | 16 | |
| β-strand | 93-94 | 2 | 10 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-41 | 34 | |
| α-helix | 47-49 | 3 | |
| α-helix | 61-63 | 3 | |
| β-strand | 70-72 | 3 | 11 |
| β-strand | 79-81 | 3 | 11 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-92 | 8 | |
Chain D: 4 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-6 | 5 | 12 |
| β-strand | 12-16 | 5 | 12 |
| β-strand | 22 | 1 | 13 |
| α-helix | 23-34 | 12 | |
| α-helix | 38-40 | 3 | |
| β-strand | 42-45 | 4 | 12 |
| β-strand | 48-49 | 2 | 12 |
| α-helix | 50-51 | 2 | |
| β-strand | 52 | 1 | 14 |
| β-strand | 54 | 1 | 14 |
| β-strand | 55 | 1 | 13 |
| α-helix | 56-59 | 4 | |
| β-strand | 66-70 | 5 | 12 |
| β-strand | 74-75 | 2 | 4 |
Chain E: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-11 | 2 | 10 |
| α-helix | 13-19 | 7 | |
| α-helix | 32-35 | 4 | |
| α-helix | 36-40 | 5 | |
| β-strand | 49 | 1 | 6 |
| α-helix | 51-57 | 7 | |
| β-strand | 58 | 1 | 8 |
| β-strand | 75-78 | 4 | 3 |
| β-strand | 84-86 | 3 | 3 |
| α-helix | 87-89 | 3 | |
| α-helix | 90-93 | 4 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin carboxyl-terminal hydrolase 8 | A | protein | 476 | Saccharomyces cerevisiae S288c | P50102 (AlphaFold model) |
| Transcription and mRNA export factor SUS1 | B | protein | 96 | Saccharomyces cerevisiae S288c | Q6WNK7 (AlphaFold model) |
| SAGA-associated factor 11 | C | protein | 99 | Saccharomyces cerevisiae S288c | Q03067 (AlphaFold model) |
| Polyubiquitin-C | D | protein | 76 | Homo sapiens | P0CG48 (AlphaFold model) |
| SAGA-associated factor 73 | E | protein | 96 | Saccharomyces cerevisiae S288c | P53165 |
Sequence of entity 1 (A), FASTA
>6AQR_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A)
GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSG
ATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILA
KYWDDVCTKTMVPSMERRDGLSGLINMGSTAFMSSILQCLIHNPYFIRHSMSQIHSNNCK
VRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ
QDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNN
SKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLP
SVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIG
IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN
Sequence of entity 2 (B), FASTA
>6AQR_2 Transcription and mRNA export factor SUS1 (chains B)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ
Sequence of entity 3 (C), FASTA
>6AQR_3 SAGA-associated factor 11 (chains C)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR
Sequence of entity 4 (D), FASTA
>6AQR_4 Polyubiquitin-C (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Sequence of entity 5 (E), FASTA
>6AQR_5 SAGA-associated factor 73 (chains E)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 8 |
Primary citation
Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins. Morrow, M.E., Morgan, M.T., Clerici, M. et al. EMBO Rep (2018) 19. DOI 10.15252/embr.201745680 · PubMed
Other PDB entries of the same protein (UniProt P50102 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3MHS 1.89 Å, Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde
- 4FK5 2.03 Å, Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module
- 4WA6 2.36 Å, Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution
- 3MHH 2.45 Å, Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module
- 4FIP 2.69 Å, Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module
- 3M99 2.7 Å, Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module
- 4FJC 2.83 Å, Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module
- 6T9L 3.6 Å, SAGA DUB module bound to a ubiqitinated nucleosome
- 4ZUX 3.82 Å, SAGA DUB module Ubp8/Sgf11/Sus1/Sgf73 bound to ubiqitinated nucleosome
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