3M99: Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module

Structure of the Ubp8-Sgf11-Sgf73-Sus1 SAGA DUB module. Determined by X-ray diffraction at 2.7 Å resolution. Released 5 May 2010.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 5,557
Mol. weight: 88.08 kDa
Ligands: ZN
Released: 5 May 2010

Explore 3M99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M99 contains 33 α-helices and 30 β-strands across 4 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: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
α-helix	17-32	16
α-helix	36-40	5
β-strand	45	1	1
β-strand	52	1	1
β-strand	58-60	3	2
β-strand	66-67	2	2
α-helix	73-79	7
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	112-114	3
α-helix	118-123	6
α-helix	130-134	5
α-helix	146-156	11
α-helix	159-166	8
α-helix	171-173	3
α-helix	183-195	13
α-helix	214-226	13
α-helix	239-256	18
α-helix	274-278	5
β-strand	281-288	8	3
β-strand	297-303	7	3
β-strand	306-309	4	4
β-strand	315	1	5
α-helix	316-324	9
β-strand	327	1	3
β-strand	346-353	8	3
β-strand	357-363	7	4
β-strand	365-367	3	6
β-strand	373-375	3	6
β-strand	381	1	5
α-helix	382-383	2
β-strand	385-387	3	4
β-strand	392	1	3
β-strand	409-422	14	4
β-strand	425-433	9	4
β-strand	439-442	4	4
β-strand	447-450	4	4
α-helix	452-455	4
β-strand	460-470	11	4

Chain B: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	10-41	32
α-helix	47-49	3
β-strand	70-72	3	7
β-strand	79-81	3	7
α-helix	82-84	3
α-helix	85-92	8

Chain C: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	11-18	8
α-helix	21-35	15
α-helix	38-52	15
α-helix	58-71	14
α-helix	75-89	15
β-strand	93	1	8

Chain D: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	8
α-helix	13-18	6
α-helix	32-34	3
α-helix	36-39	4
α-helix	51-57	7
β-strand	75-77	3	9
β-strand	84-86	3	9
α-helix	90-92	3
α-helix	93-97	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 8	A	protein	471	Saccharomyces cerevisiae	P50102 (AlphaFold model)
SAGA-associated factor 11	B	protein	99	Saccharomyces cerevisiae	Q03067 (AlphaFold model)
Protein SUS1	C	protein	96	Saccharomyces cerevisiae	Q6WNK7 (AlphaFold model)
SAGA-associated factor 73	D	protein	104	Saccharomyces cerevisiae	P53165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3M99_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A)
MSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSGATFMC
LQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDD
VCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPD
KCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQQDAHE
FWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNNSKTTI
DPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLPSVLVL
QLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIGIVSHK
GTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Sequence of entity 2 (B), FASTA

>3M99_2 SAGA-associated factor 11 (chains B)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Sequence of entity 3 (C), FASTA

>3M99_3 Protein SUS1 (chains C)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Sequence of entity 4 (D), FASTA

>3M99_4 SAGA-associated factor 73 (chains D)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLENHCAGASGK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	7

Primary citation

Structural basis for assembly and activation of the heterotetrameric SAGA histone H2B deubiquitinase module. Kohler, A., Zimmerman, E., Schneider, M. et al. Cell (2010) 141:606-617. DOI 10.1016/j.cell.2010.04.026 · 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
6AQR 2.1 Å, SAGA DUB module Ubp8(C146A)/Sgf11/Sus1/Sgf73 bound to monoubiquitin
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
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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