4FJC: Ubiquitin carboxyl-terminal hydrolase 8

Name: PDB 4FJC: Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module
Published: 2012-07-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: hydrolase

Structure of the SAGA Ubp8/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module. Determined by X-ray diffraction at 2.83 Å resolution. Released 25 Jul 2012.

Method: X-ray diffraction
Resolution: 2.83 Å
Organism: Saccharomyces cerevisiae
Chains: 8
Atoms: 10,581
Mol. weight: 175.51 kDa
Ligands: ZN
Released: 25 Jul 2012

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

Secondary structure: helices and β-sheets

4FJC contains 58 α-helices and 65 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	5-10	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	146-155	10
α-helix	159-166	8
α-helix	169-173	5
α-helix	183-195	13
α-helix	214-226	13
α-helix	238-255	18
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	316-324	9
β-strand	327-329	3	4
α-helix	344	1
β-strand	345-353	9	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	426-434	9	5
β-strand	438-443	6	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	21-36	16
α-helix	38-52	15
α-helix	58-71	14
α-helix	75-92	18
β-strand	93-95	3	9

Chain C: 1 helix, 1 β-strand

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

Chain D: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	10
β-strand	8-11	4	9
α-helix	13-18	6
α-helix	32-35	4
α-helix	36-40	5
β-strand	46	1	11
β-strand	49	1	11
α-helix	51-57	7
β-strand	58	1	12
β-strand	75-78	4	3
β-strand	84-86	3	3
α-helix	87-94	8

Chain E: 16 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
α-helix	14-32	19
α-helix	36-42	7
β-strand	45	1	13
β-strand	52	1	13
β-strand	57-60	4	14
β-strand	66-68	3	14
α-helix	73-81	9
β-strand	85-88	4	14
β-strand	94-96	3	14
β-strand	101-102	2	14
α-helix	107-110	4
α-helix	112-117	6
α-helix	118-124	7
β-strand	125-126	2	15
α-helix	127-129	3
α-helix	146-155	10
α-helix	159-166	8
α-helix	183-195	13
α-helix	214-226	13
α-helix	238-255	18
β-strand	281-288	8	16
β-strand	295-303	9	16
β-strand	305-309	5	11
β-strand	315	1	17
α-helix	316-323	8
β-strand	326-336	11	16
β-strand	341-353	13	16
β-strand	354	1	12
β-strand	357-363	7	11
β-strand	365	1	18
β-strand	375	1	18
β-strand	381	1	17
β-strand	385-387	3	11
α-helix	389-391	3
β-strand	392	1	16
β-strand	409-420	12	11
β-strand	427-433	7	11
β-strand	439-443	5	11
β-strand	446-450	5	11
α-helix	452-455	4
β-strand	460-470	11	11

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-19	10
α-helix	21-36	16
α-helix	38-52	15
α-helix	58-72	15
α-helix	75-92	18

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-41	34

Chain H: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	15-17	3
α-helix	32-35	4
α-helix	36-41	6
β-strand	49	1	5
α-helix	51-57	7
β-strand	58	1	7
β-strand	75-78	4	15
β-strand	84-86	3	15
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, E	protein	476	Saccharomyces cerevisiae	P50102 (AlphaFold model)
Protein SUS1	B, F	protein	96	Saccharomyces cerevisiae	Q6WNK7 (AlphaFold model)
SAGA-associated factor 11	C, G	protein	99	Saccharomyces cerevisiae	Q03067 (AlphaFold model)
SAGA-associated factor 73	D, H	protein	96	Saccharomyces cerevisiae	P53165 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>4FJC_1 Ubiquitin carboxyl-terminal hydrolase 8 (chains A, E)
GAAAAMSICPHIQQVFQNEKSKDGVLKTCNAARYILNHSVPKEKFLNTMKCGTCHEINSG
ATFMCLQCGFCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILA
KYWDDVCTKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCK
VRSPDKCFSCALDKIVHELYGALNTKQASSSSTSTNRQTGFIYLLTCAWKINQNLAGYSQ
QDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEGSLESSIVCPGCQNN
SKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQLKDFNYHCGECNSTQDAIKQLGIHKLP
SVLVLQLKRFEHLLNGSNRKLDDFIEFPTYLNMKNYCSTKEKDKHSENGKVPDIIYELIG
IVSHKGTVNEGHYIAFCKISGGQWFKFNDSMVSSISQEEVLKEQAYLLFYTIRQVN

Sequence of entity 2 (B, F), FASTA

>4FJC_2 Protein SUS1 (chains B, F)
MTMDTAQLKSQIQQYLVESGNYELISNELKARLLQEGWVDKVKDLTKSEMNINESTNFTQ
ILSTVEPKALEMVSDSTRETVLKQIREFLEEIVDTQ

Sequence of entity 3 (C, G), FASTA

>4FJC_3 SAGA-associated factor 11 (chains C, G)
MTEETITIDSISNGILNNLLTTLIQDIVARETTQQQLLKTRYPDLRSYYFDPNGSLDING
LQKQQESSQYIHCENCGRDVSANRLAAHLQRCLSRGARR

Sequence of entity 4 (D, H), FASTA

>4FJC_4 SAGA-associated factor 73 (chains D, H)
MRSGDAEIKGIKPKVIEEYSLSQGSGPSNDSWKSLMSSAKDTPLQYDHMNRESLKKYFNP
NAQLIEDPLDKPIQYRVCEKCGKPLALTAIVDHLEN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Water and common crystallization additives (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
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
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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