4FK5: SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module

Structure of the SAGA Ubp8(S144N)/Sgf11/Sus1/Sgf73 DUB module. Determined by X-ray diffraction at 2.03 Å resolution. Released 25 Jul 2012.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Saccharomyces cerevisiae
Chains: 4
Atoms: 6,139
Mol. weight: 88.05 kDa
Ligands: ZN
Released: 25 Jul 2012

Explore 4FK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FK5 contains 40 α-helices and 38 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: 20 helices, 26 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	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	238-256	19
α-helix	260-267	8
α-helix	274-278	5
β-strand	281-288	8	4
β-strand	295-303	9	4
β-strand	306-308	3	5
β-strand	315	1	6
α-helix	316-323	8
β-strand	327	1	4
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	409-420	12	5
β-strand	427-433	7	5
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	8-18	11
α-helix	21-35	15
α-helix	38-53	16
α-helix	58-72	15
α-helix	75-90	16
β-strand	93-95	3	9

Chain C: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	10
α-helix	8-41	34
α-helix	47-49	3
β-strand	56	1	11
β-strand	62	1	11
α-helix	63-64	2
α-helix	66-68	3
β-strand	70-72	3	12
β-strand	79-81	3	12
α-helix	82-84	3
α-helix	85-94	10

Chain E: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6	1
β-strand	7	1	10
β-strand	8-11	4	9
α-helix	13-18	6
α-helix	27-28	2
α-helix	32-35	4
α-helix	36-41	6
α-helix	43-44	2
β-strand	49	1	5
α-helix	51-57	7
β-strand	58	1	7
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	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)
SAGA-associated factor 73	E	protein	96	Saccharomyces cerevisiae	P53165 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4FK5_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A)
GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSG
ATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILA
KYWDDVCTKTMVPSMERRDGLSGLINMGNTCFMSSILQCLIHNPYFIRHSMSQIHSNNCK
VRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ
QDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNN
SKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLP
SVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIG
IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Sequence of entity 2 (B), FASTA

>4FK5_2 Protein SUS1 (chains B)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Sequence of entity 3 (C), FASTA

>4FK5_3 SAGA-associated factor 11 (chains C)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Sequence of entity 4 (E), FASTA

>4FK5_4 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

A Role for Intersubunit Interactions in Maintaining SAGA Deubiquitinating Module Structure and Activity. Samara, N.L., Ringel, A.E., Wolberger, C. Structure (2012) 20:1414-1424. DOI 10.1016/j.str.2012.05.015 · 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
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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