Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3MHS

Structure of the SAGA Ubp8/Sgf11/Sus1/Sgf73 DUB module bound to ubiquitin aldehyde

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000124	cellular_component	SAGA complex
A	0004843	molecular_function	cysteine-type deubiquitinase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0006508	biological_process	proteolysis
A	0008233	molecular_function	peptidase activity
A	0008234	molecular_function	cysteine-type peptidase activity
A	0008270	molecular_function	zinc ion binding
A	0008380	biological_process	RNA splicing
A	0016579	biological_process	protein deubiquitination
A	0016787	molecular_function	hydrolase activity
A	0046695	cellular_component	SLIK (SAGA-like) complex
A	0046872	molecular_function	metal ion binding
A	0060090	molecular_function	molecular adaptor activity
A	0071819	cellular_component	DUBm complex
B	0000124	cellular_component	SAGA complex
B	0000932	cellular_component	P-body
B	0000973	biological_process	post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery
B	0003682	molecular_function	chromatin binding
B	0003713	molecular_function	transcription coactivator activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005643	cellular_component	nuclear pore
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0006325	biological_process	chromatin organization
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0006406	biological_process	mRNA export from nucleus
B	0008047	molecular_function	enzyme activator activity
B	0015031	biological_process	protein transport
B	0016973	biological_process	poly(A)+ mRNA export from nucleus
B	0032880	biological_process	regulation of protein localization
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045944	biological_process	positive regulation of transcription by RNA polymerase II
B	0046695	cellular_component	SLIK (SAGA-like) complex
B	0051028	biological_process	mRNA transport
B	0070390	cellular_component	transcription export complex 2
B	0071028	biological_process	nuclear mRNA surveillance
B	0071819	cellular_component	DUBm complex
C	0000124	cellular_component	SAGA complex
C	0003713	molecular_function	transcription coactivator activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0006325	biological_process	chromatin organization
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0008047	molecular_function	enzyme activator activity
C	0008270	molecular_function	zinc ion binding
C	0045893	biological_process	positive regulation of DNA-templated transcription
C	0046695	cellular_component	SLIK (SAGA-like) complex
C	0046872	molecular_function	metal ion binding
C	0070461	cellular_component	SAGA-type complex
C	0071819	cellular_component	DUBm complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 1295

Chain	Residue
A	GLN236
A	GLU240
D	ARG74

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 1487

Chain	Residue
A	HIS367
A	LEU369
A	GLY371
A	HOH562
D	GLY35

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 472

Chain	Residue
A	HIS6
A	CYS96
A	CYS99
A	CYS4

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 473

Chain	Residue
A	CYS46
A	CYS49
A	CYS68
A	HIS73

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 474

Chain	Residue
A	CYS60
A	CYS63
A	HIS77
A	HIS83

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 475

Chain	Residue
A	HIS170
A	CYS174
A	CYS182
A	CYS185

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 476

Chain	Residue
A	HIS250
A	CYS271
A	CYS273
A	HIS276

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN C 100

Chain	Residue
C	CYS73
C	CYS76
C	HIS88
C	CYS92

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN E 97

Chain	Residue
E	CYS78
E	CYS81
E	HIS93
E	GLU95

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 477

Chain	Residue
A	CYS289
A	CYS292
A	CYS336
A	CYS339

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
D	LYS27-ASP52

site_id	PS00972
Number of Residues	16
Details	USP_1 Ubiquitin specific protease (USP) domain signature 1. GLinmGStCFMSSiLQ

Chain	Residue	Details
A	GLY138-GLN153

site_id	PS00973
Number of Residues	18
Details	USP_2 Ubiquitin specific protease (USP) domain signature 2. YeLiGIvsHkGtvne..GHY

Chain	Residue	Details
A	TYR411-TYR428

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	100
Details	Zinc finger: {"description":"UBP-type; degenerate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00502","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	1
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU01035","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PROSITE-ProRule","id":"PRU01035","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	17
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3M99","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MHH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FK5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4WA6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZUX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6AQR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3M99","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FJC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FIP","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FK5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZUX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6AQR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZUX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6AQR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	21
Details	Zinc finger: {"description":"SGF11-type","evidences":[{"source":"HAMAP-Rule","id":"MF_03047","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3M99","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MHH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FK5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZUX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6AQR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4ZUX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Site: {"description":"Interacts with activating enzyme"}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	1
Details	Site: {"description":"Essential for function"}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20395473","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20434206","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3M99","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MHH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3MHS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FIP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FJC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FK5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4W4U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4WA6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4ZUX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6AQR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)