4WA6: Yeast SAGA DUBm with Sgf73 N59D mutant
Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution. Determined by X-ray diffraction at 2.36 Å resolution. Released 4 Mar 2015.
- Method
- X-ray diffraction
- Resolution
- 2.36 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 8
- Atoms
- 11,129
- Mol. weight
- 175.48 kDa
- Ligands
- ZN
- Released
- 4 Mar 2015
Explore 4WA6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4WA6 contains 75 α-helices and 71 β-strands across 8 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: 24 helices, 26 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| 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 | 146-156 | 11 | |
| α-helix | 159-166 | 8 | |
| α-helix | 169-173 | 5 | |
| α-helix | 183-195 | 13 | |
| α-helix | 214-224 | 11 | |
| α-helix | 238-255 | 18 | |
| α-helix | 260-268 | 9 | |
| α-helix | 274-278 | 5 | |
| β-strand | 281-288 | 8 | 4 |
| β-strand | 299-303 | 5 | 4 |
| β-strand | 306-308 | 3 | 5 |
| β-strand | 315 | 1 | 6 |
| α-helix | 316-324 | 9 | |
| β-strand | 327-328 | 2 | 4 |
| α-helix | 329-330 | 2 | |
| α-helix | 344-345 | 2 | |
| β-strand | 346-353 | 8 | 4 |
| β-strand | 354 | 1 | 7 |
| β-strand | 357-362 | 6 | 5 |
| β-strand | 365-367 | 3 | 8 |
| β-strand | 373-375 | 3 | 8 |
| β-strand | 381 | 1 | 6 |
| β-strand | 385-387 | 3 | 5 |
| α-helix | 389-391 | 3 | |
| β-strand | 392 | 1 | 4 |
| α-helix | 406-408 | 3 | |
| β-strand | 409-421 | 13 | 5 |
| β-strand | 426-433 | 8 | 5 |
| α-helix | 435-437 | 3 | |
| β-strand | 439-443 | 5 | 5 |
| β-strand | 446-450 | 5 | 5 |
| α-helix | 452-455 | 4 | |
| β-strand | 460-470 | 11 | 5 |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-19 | 15 | |
| α-helix | 21-35 | 15 | |
| α-helix | 38-53 | 16 | |
| α-helix | 58-72 | 15 | |
| α-helix | 75-92 | 18 | |
| β-strand | 93-95 | 3 | 9 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 10 |
| α-helix | 8-41 | 34 | |
| α-helix | 45-49 | 5 | |
| α-helix | 62-65 | 4 | |
| β-strand | 70 | 1 | 11 |
| β-strand | 81 | 1 | 11 |
| α-helix | 82-84 | 3 | |
| α-helix | 85-92 | 8 | |
Chain D: 22 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| α-helix | 5-10 | 6 | |
| α-helix | 14-32 | 19 | |
| α-helix | 36-43 | 8 | |
| β-strand | 45 | 1 | 12 |
| β-strand | 52 | 1 | 12 |
| β-strand | 57-60 | 4 | 13 |
| β-strand | 66-68 | 3 | 13 |
| α-helix | 73-81 | 9 | |
| β-strand | 85-88 | 4 | 13 |
| β-strand | 93-96 | 4 | 13 |
| β-strand | 101-102 | 2 | 13 |
| α-helix | 107-110 | 4 | |
| α-helix | 112-117 | 6 | |
| α-helix | 118-124 | 7 | |
| β-strand | 125-126 | 2 | 14 |
| α-helix | 127-129 | 3 | |
| α-helix | 146-156 | 11 | |
| α-helix | 159-166 | 8 | |
| α-helix | 169-173 | 5 | |
| α-helix | 183-195 | 13 | |
| α-helix | 214-224 | 11 | |
| α-helix | 238-255 | 18 | |
| α-helix | 260-267 | 8 | |
| α-helix | 274-278 | 5 | |
| β-strand | 281-286 | 6 | 15 |
| β-strand | 298-303 | 6 | 15 |
| β-strand | 306-308 | 3 | 16 |
| β-strand | 315 | 1 | 17 |
| α-helix | 316-324 | 9 | |
| β-strand | 348-353 | 6 | 15 |
| β-strand | 354 | 1 | 18 |
| β-strand | 357-362 | 6 | 16 |
| β-strand | 365-367 | 3 | 19 |
| β-strand | 373-375 | 3 | 19 |
| β-strand | 381 | 1 | 17 |
| β-strand | 385-387 | 3 | 16 |
| α-helix | 389-391 | 3 | |
| β-strand | 392 | 1 | 15 |
| α-helix | 406-408 | 3 | |
| β-strand | 409-421 | 13 | 16 |
| β-strand | 426-433 | 8 | 16 |
| α-helix | 434 | 1 | |
| β-strand | 439-443 | 5 | 16 |
| β-strand | 446-450 | 5 | 16 |
| α-helix | 452-456 | 5 | |
| β-strand | 462-470 | 9 | 16 |
Chain E: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 10 |
| β-strand | 8-11 | 4 | 9 |
| α-helix | 13-16 | 4 | |
| α-helix | 32-35 | 4 | |
| α-helix | 36-40 | 5 | |
| β-strand | 49 | 1 | 5 |
| α-helix | 51-57 | 7 | |
| β-strand | 58 | 1 | 7 |
| α-helix | 68-70 | 3 | |
| α-helix | 72-74 | 3 | |
| β-strand | 75-78 | 4 | 3 |
| β-strand | 84-86 | 3 | 3 |
| α-helix | 87-94 | 8 | |
Chain F: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-19 | 16 | |
| α-helix | 21-35 | 15 | |
| α-helix | 38-52 | 15 | |
| α-helix | 58-71 | 14 | |
| α-helix | 75-92 | 18 | |
| β-strand | 93-94 | 2 | 20 |
Chain G: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 21 |
| α-helix | 8-41 | 34 | |
| β-strand | 71-73 | 3 | 22 |
| β-strand | 78-80 | 3 | 22 |
| α-helix | 85-92 | 8 | |
Chain H: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 21 |
| β-strand | 10-11 | 2 | 20 |
| α-helix | 13-16 | 4 | |
| α-helix | 32-34 | 3 | |
| α-helix | 35-40 | 6 | |
| β-strand | 49 | 1 | 16 |
| α-helix | 51-57 | 7 | |
| β-strand | 58 | 1 | 18 |
| β-strand | 75-78 | 4 | 14 |
| β-strand | 84-86 | 3 | 14 |
| α-helix | 87-95 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ubiquitin carboxyl-terminal hydrolase 8 | A, D | protein | 476 | Saccharomyces cerevisiae | P50102 (AlphaFold model) |
| Transcription and mRNA export factor SUS1 | B, F | protein | 96 | Saccharomyces cerevisiae | Q6WNK7 (AlphaFold model) |
| SAGA-associated factor 11 | C, G | protein | 99 | Saccharomyces cerevisiae | A6ZWK1 (AlphaFold model) |
| SAGA-associated factor 73 | E, H | protein | 96 | Saccharomyces cerevisiae | P53165 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>4WA6_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A, D)
GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSG
ATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILA
KYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCK
VRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ
QDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNN
SKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLP
SVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIG
IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN
Sequence of entity 2 (B, F), FASTA
>4WA6_2 Transcription and mRNA export factor SUS1 (chains B, F)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ
Sequence of entity 3 (C, G), FASTA
>4WA6_3 SAGA-associated factor 11 (chains C, G)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR
Sequence of entity 4 (E, H), FASTA
>4WA6_4 SAGA-associated factor 73 (chains E, H)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFDP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 15 |
Primary citation
Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution. Wolberger, C., Yan, M. To be published.
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
- 6AQR 2.1 Å, SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin
- 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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