3MHS: SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde. Determined by X-ray diffraction at 1.89 Å resolution. Released 21 Apr 2010.

Method: X-ray diffraction
Resolution: 1.89 Å
Organisms: Saccharomyces cerevisiae, Homo sapiens
Chains: 5
Atoms: 7,460
Mol. weight: 96.49 kDa
Ligands: ZN
Released: 21 Apr 2010

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

Secondary structure: helices and β-sheets

3MHS contains 44 α-helices and 49 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: 24 helices, 31 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
α-helix	93	1
β-strand	94-96	3	2
β-strand	101-103	3	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
α-helix	274-278	5
β-strand	281-288	8	5
β-strand	297-303	7	5
β-strand	306-308	3	6
β-strand	315	1	7
α-helix	316-324	9
β-strand	327-328	2	5
β-strand	335-336	2	8
β-strand	341-342	2	8
β-strand	346-353	8	5
β-strand	354	1	9
β-strand	357-362	6	6
β-strand	365-367	3	10
β-strand	373-375	3	10
β-strand	381	1	7
β-strand	385-387	3	6
α-helix	389-391	3
β-strand	392	1	5
α-helix	395	1
β-strand	396	1	11
α-helix	397	1
β-strand	405	1	11
α-helix	406-408	3
β-strand	409-421	13	6
β-strand	426-433	8	6
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	7-18	12
α-helix	21-35	15
α-helix	38-53	16
α-helix	58-71	14
α-helix	75-92	18
β-strand	93-94	2	12

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	13
α-helix	8-41	34
α-helix	47-49	3
α-helix	62-64	3
β-strand	70-72	3	14
β-strand	79-81	3	14
α-helix	82-84	3
α-helix	85-92	8

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	15
β-strand	12-16	5	15
β-strand	22	1	16
α-helix	23-34	12
α-helix	38-40	3
β-strand	42-45	4	15
β-strand	48-49	2	15
β-strand	55	1	16
α-helix	57-59	3
β-strand	66-70	5	15
β-strand	74-75	2	4

Chain E: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	13
β-strand	10-11	2	12
α-helix	13-18	6
α-helix	32-35	4
α-helix	36-41	6
α-helix	43-44	2
β-strand	49	1	6
α-helix	51-57	7
β-strand	58	1	9
α-helix	73-74	2
β-strand	76-78	3	3
β-strand	84-85	2	3
α-helix	87-89	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase 8	A	protein	476	Saccharomyces cerevisiae	P50102 (AlphaFold model)
Protein SUS1	B	protein	96	Saccharomyces cerevisiae	Q6WNK7 (AlphaFold model)
SAGA-associated factor 11	C	protein	99	Saccharomyces cerevisiae	Q03067 (AlphaFold model)
Ubiquitin	D	protein	76	Homo sapiens	P0CG48 (AlphaFold model)
SAGA-associated factor 73	E	protein	96	Saccharomyces cerevisiae	P53165

Sequence of entity 1 (A), FASTA

>3MHS_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A)
GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSG
ATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILA
KYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCK
VRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ
QDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNN
SKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLP
SVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIG
IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Sequence of entity 2 (B), FASTA

>3MHS_2 Protein SUS1 (chains B)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Sequence of entity 3 (C), FASTA

>3MHS_3 SAGA-associated factor 11 (chains C)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Sequence of entity 4 (D), FASTA

>3MHS_4 Ubiquitin (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 5 (E), FASTA

>3MHS_5 SAGA-associated factor 73 (chains E)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Water and common crystallization additives (EDO, GOL) are not listed.

Primary citation

Structural insights into the assembly and function of the SAGA deubiquitinating module. Samara, N.L., Datta, A.B., Berndsen, C.E. et al. Science (2010) 328:1025-1029. DOI 10.1126/science.1190049 · PubMed

Other PDB entries of the same protein (UniProt P50102 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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
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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