4W4U: Yeast SAGA DUBm with Sgf73 Y57A mutant

Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution. Determined by X-ray diffraction at 2.8 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 10,594
Mol. weight: 175.17 kDa
Ligands: ZN
Released: 1 Jul 2015

Explore 4W4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4W4U contains 62 α-helices and 68 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: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
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	146-155	10
α-helix	159-166	8
α-helix	183-195	13
α-helix	214-224	11
α-helix	238-256	19
α-helix	260-268	9
α-helix	274-278	5
β-strand	281-288	8	4
α-helix	290-292	3
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
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
β-strand	409-421	13	5
β-strand	426-433	8	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	5-19	15
α-helix	21-36	16
α-helix	38-53	16
α-helix	58-72	15
α-helix	75-92	18
β-strand	93-95	3	9

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	10
α-helix	8-41	34
α-helix	47-49	3

Chain D: 19 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
α-helix	14-32	19
α-helix	36-43	8
β-strand	45	1	11
β-strand	52	1	11
β-strand	57-60	4	12
β-strand	66-68	3	12
α-helix	73-81	9
β-strand	85-88	4	12
β-strand	94-96	3	12
β-strand	101-102	2	12
α-helix	107-110	4
α-helix	112-117	6
α-helix	118-124	7
β-strand	125-126	2	13
α-helix	127-129	3
α-helix	146-155	10
α-helix	159-166	8
α-helix	183-195	13
α-helix	217-224	8
α-helix	238-256	19
α-helix	260-267	8
α-helix	274-278	5
β-strand	281-287	7	14
β-strand	299-303	5	14
β-strand	306-309	4	15
β-strand	315	1	16
α-helix	316-324	9
β-strand	327	1	14
β-strand	347-353	7	14
β-strand	354	1	17
β-strand	357-363	7	15
β-strand	365-367	3	18
α-helix	368	1
β-strand	373-375	3	18
β-strand	381	1	16
β-strand	385-387	3	15
α-helix	389-391	3
β-strand	392	1	14
β-strand	409-421	13	15
β-strand	426-433	8	15
β-strand	439-443	5	15
β-strand	446-450	5	15
α-helix	452-455	4
β-strand	460-470	11	15

Chain E: 6 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	13-16	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
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	21-36	16
α-helix	38-53	16
α-helix	58-72	15
α-helix	75-92	18
β-strand	93-95	3	19

Chain G: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	20
α-helix	8-41	34

Chain H: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	20
β-strand	8-11	4	19
α-helix	13-16	4
α-helix	32-35	4
α-helix	36-40	5
β-strand	49	1	15
α-helix	51-57	7
β-strand	58	1	17
β-strand	75-78	4	13
β-strand	84-86	3	13
α-helix	87-95	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin carboxyl-terminal hydrolase	A, D	protein	476	Saccharomyces cerevisiae	N1P0J5 (AlphaFold model)
Transcription and mRNA export factor SUS1	B, F	protein	96	Saccharomyces cerevisiae	N1P8F5 (AlphaFold model)
SAGA-associated factor 11	C, G	protein	99	Saccharomyces cerevisiae	N1NXA6 (AlphaFold model)
SAGA-associated factor 73	E, H	protein	96	Saccharomyces cerevisiae	P53165 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4W4U_1 Ubiquitin carboxyl-terminal hydrolase (chains A, D)
GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSG
ATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILA
KYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCK
VRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ
QDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNN
SKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLP
SVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIG
IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Sequence of entity 2 (B, F), FASTA

>4W4U_2 Transcription and mRNA export factor SUS1 (chains B, F)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Sequence of entity 3 (C, G), FASTA

>4W4U_3 SAGA-associated factor 11 (chains C, G)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Sequence of entity 4 (E, H), FASTA

>4W4U_4 SAGA-associated factor 73 (chains E, H)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKAFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	13

Primary citation

Uncovering the role of Sgf73 in maintaining SAGA deubiquitinating module structure and activity. Yan, M., Wolberger, C. J Mol Biol (2015) 427:1765-1778. DOI 10.1016/j.jmb.2014.12.004 · PubMed

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