6EF3

Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state)

Functional Information from GO Data

Chain	GOid	namespace	contents
1	0000502	cellular_component	proteasome complex
1	0004175	molecular_function	endopeptidase activity
1	0004298	molecular_function	threonine-type endopeptidase activity
1	0005515	molecular_function	protein binding
1	0005634	cellular_component	nucleus
1	0005737	cellular_component	cytoplasm
1	0005829	cellular_component	cytosol
1	0005839	cellular_component	proteasome core complex
1	0006508	biological_process	proteolysis
1	0008233	molecular_function	peptidase activity
1	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
1	0016787	molecular_function	hydrolase activity
1	0019774	cellular_component	proteasome core complex, beta-subunit complex
1	0034515	cellular_component	proteasome storage granule
1	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
1	0051603	biological_process	proteolysis involved in protein catabolic process
2	0000502	cellular_component	proteasome complex
2	0004175	molecular_function	endopeptidase activity
2	0004298	molecular_function	threonine-type endopeptidase activity
2	0005515	molecular_function	protein binding
2	0005634	cellular_component	nucleus
2	0005737	cellular_component	cytoplasm
2	0005829	cellular_component	cytosol
2	0005839	cellular_component	proteasome core complex
2	0006508	biological_process	proteolysis
2	0008233	molecular_function	peptidase activity
2	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
2	0016787	molecular_function	hydrolase activity
2	0019774	cellular_component	proteasome core complex, beta-subunit complex
2	0034515	cellular_component	proteasome storage granule
2	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
2	0051603	biological_process	proteolysis involved in protein catabolic process
3	0000502	cellular_component	proteasome complex
3	0005515	molecular_function	protein binding
3	0005634	cellular_component	nucleus
3	0005737	cellular_component	cytoplasm
3	0005829	cellular_component	cytosol
3	0005839	cellular_component	proteasome core complex
3	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
3	0019774	cellular_component	proteasome core complex, beta-subunit complex
3	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
3	0051603	biological_process	proteolysis involved in protein catabolic process
3	0061133	molecular_function	endopeptidase activator activity
4	0000502	cellular_component	proteasome complex
4	0005515	molecular_function	protein binding
4	0005634	cellular_component	nucleus
4	0005737	cellular_component	cytoplasm
4	0005789	cellular_component	endoplasmic reticulum membrane
4	0005829	cellular_component	cytosol
4	0005839	cellular_component	proteasome core complex
4	0010498	biological_process	proteasomal protein catabolic process
4	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
4	0019774	cellular_component	proteasome core complex, beta-subunit complex
4	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
4	0051603	biological_process	proteolysis involved in protein catabolic process
4	0061133	molecular_function	endopeptidase activator activity
5	0000502	cellular_component	proteasome complex
5	0004175	molecular_function	endopeptidase activity
5	0004298	molecular_function	threonine-type endopeptidase activity
5	0005515	molecular_function	protein binding
5	0005634	cellular_component	nucleus
5	0005737	cellular_component	cytoplasm
5	0005777	cellular_component	peroxisome
5	0005829	cellular_component	cytosol
5	0005839	cellular_component	proteasome core complex
5	0006508	biological_process	proteolysis
5	0008233	molecular_function	peptidase activity
5	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
5	0016787	molecular_function	hydrolase activity
5	0019774	cellular_component	proteasome core complex, beta-subunit complex
5	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
5	0051603	biological_process	proteolysis involved in protein catabolic process
5	0080129	biological_process	proteasome core complex assembly
6	0000502	cellular_component	proteasome complex
6	0003674	molecular_function	molecular_function
6	0005515	molecular_function	protein binding
6	0005634	cellular_component	nucleus
6	0005737	cellular_component	cytoplasm
6	0005829	cellular_component	cytosol
6	0005839	cellular_component	proteasome core complex
6	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
6	0019774	cellular_component	proteasome core complex, beta-subunit complex
6	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
6	0051603	biological_process	proteolysis involved in protein catabolic process
7	0000502	cellular_component	proteasome complex
7	0003674	molecular_function	molecular_function
7	0005515	molecular_function	protein binding
7	0005634	cellular_component	nucleus
7	0005737	cellular_component	cytoplasm
7	0005829	cellular_component	cytosol
7	0005839	cellular_component	proteasome core complex
7	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
7	0019774	cellular_component	proteasome core complex, beta-subunit complex
7	0034515	cellular_component	proteasome storage granule
7	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
7	0043248	biological_process	proteasome assembly
7	0051603	biological_process	proteolysis involved in protein catabolic process
A	0000502	cellular_component	proteasome complex
A	0003674	molecular_function	molecular_function
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0005839	cellular_component	proteasome core complex
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
A	0019773	cellular_component	proteasome core complex, alpha-subunit complex
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0051603	biological_process	proteolysis involved in protein catabolic process
B	0000502	cellular_component	proteasome complex
B	0003674	molecular_function	molecular_function
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005839	cellular_component	proteasome core complex
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
B	0019773	cellular_component	proteasome core complex, alpha-subunit complex
B	0034515	cellular_component	proteasome storage granule
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0051603	biological_process	proteolysis involved in protein catabolic process
C	0000502	cellular_component	proteasome complex
C	0003674	molecular_function	molecular_function
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005839	cellular_component	proteasome core complex
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
C	0019773	cellular_component	proteasome core complex, alpha-subunit complex
C	0034515	cellular_component	proteasome storage granule
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0051603	biological_process	proteolysis involved in protein catabolic process
C	0080129	biological_process	proteasome core complex assembly
D	0000502	cellular_component	proteasome complex
D	0003674	molecular_function	molecular_function
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005839	cellular_component	proteasome core complex
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
D	0019773	cellular_component	proteasome core complex, alpha-subunit complex
D	0034515	cellular_component	proteasome storage granule
D	0042175	cellular_component	nuclear outer membrane-endoplasmic reticulum membrane network
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0051603	biological_process	proteolysis involved in protein catabolic process
E	0000502	cellular_component	proteasome complex
E	0003674	molecular_function	molecular_function
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005839	cellular_component	proteasome core complex
E	0006511	biological_process	ubiquitin-dependent protein catabolic process
E	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
E	0019773	cellular_component	proteasome core complex, alpha-subunit complex
E	0034515	cellular_component	proteasome storage granule
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0051603	biological_process	proteolysis involved in protein catabolic process
F	0000502	cellular_component	proteasome complex
F	0003674	molecular_function	molecular_function
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005839	cellular_component	proteasome core complex
F	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
F	0019773	cellular_component	proteasome core complex, alpha-subunit complex
F	0034515	cellular_component	proteasome storage granule
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0051603	biological_process	proteolysis involved in protein catabolic process
G	0000502	cellular_component	proteasome complex
G	0003729	molecular_function	mRNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005839	cellular_component	proteasome core complex
G	0006511	biological_process	ubiquitin-dependent protein catabolic process
G	0010499	biological_process	proteasomal ubiquitin-independent protein catabolic process
G	0019773	cellular_component	proteasome core complex, alpha-subunit complex
G	0034515	cellular_component	proteasome storage granule
G	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
G	0051603	biological_process	proteolysis involved in protein catabolic process
H	0000166	molecular_function	nucleotide binding
H	0000502	cellular_component	proteasome complex
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0006511	biological_process	ubiquitin-dependent protein catabolic process
H	0008540	cellular_component	proteasome regulatory particle, base subcomplex
H	0010498	biological_process	proteasomal protein catabolic process
H	0010604	biological_process	positive regulation of macromolecule metabolic process
H	0016887	molecular_function	ATP hydrolysis activity
H	0031625	molecular_function	ubiquitin protein ligase binding
H	0036402	molecular_function	proteasome-activating activity
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0045732	biological_process	positive regulation of protein catabolic process
H	0045899	biological_process	positive regulation of RNA polymerase II transcription preinitiation complex assembly
H	0070682	biological_process	proteasome regulatory particle assembly
H	0080090	biological_process	regulation of primary metabolic process
H	1901800	biological_process	positive regulation of proteasomal protein catabolic process
I	0000166	molecular_function	nucleotide binding
I	0000502	cellular_component	proteasome complex
I	0005515	molecular_function	protein binding
I	0005524	molecular_function	ATP binding
I	0005634	cellular_component	nucleus
I	0005737	cellular_component	cytoplasm
I	0006511	biological_process	ubiquitin-dependent protein catabolic process
I	0008540	cellular_component	proteasome regulatory particle, base subcomplex
I	0010498	biological_process	proteasomal protein catabolic process
I	0010604	biological_process	positive regulation of macromolecule metabolic process
I	0016887	molecular_function	ATP hydrolysis activity
I	0031503	biological_process	protein-containing complex localization
I	0036402	molecular_function	proteasome-activating activity
I	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
I	0043171	biological_process	peptide catabolic process
I	0045732	biological_process	positive regulation of protein catabolic process
I	0070651	biological_process	nonfunctional rRNA decay
I	0070682	biological_process	proteasome regulatory particle assembly
I	0080090	biological_process	regulation of primary metabolic process
I	1901800	biological_process	positive regulation of proteasomal protein catabolic process
J	0000166	molecular_function	nucleotide binding
J	0000502	cellular_component	proteasome complex
J	0005515	molecular_function	protein binding
J	0005524	molecular_function	ATP binding
J	0005634	cellular_component	nucleus
J	0005737	cellular_component	cytoplasm
J	0006289	biological_process	nucleotide-excision repair
J	0006338	biological_process	chromatin remodeling
J	0008540	cellular_component	proteasome regulatory particle, base subcomplex
J	0010498	biological_process	proteasomal protein catabolic process
J	0010604	biological_process	positive regulation of macromolecule metabolic process
J	0016887	molecular_function	ATP hydrolysis activity
J	0019904	molecular_function	protein domain specific binding
J	0031625	molecular_function	ubiquitin protein ligase binding
J	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
J	0034515	cellular_component	proteasome storage granule
J	0036402	molecular_function	proteasome-activating activity
J	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
J	0045899	biological_process	positive regulation of RNA polymerase II transcription preinitiation complex assembly
J	0070651	biological_process	nonfunctional rRNA decay
J	0070682	biological_process	proteasome regulatory particle assembly
J	0080090	biological_process	regulation of primary metabolic process
J	1901800	biological_process	positive regulation of proteasomal protein catabolic process
K	0000166	molecular_function	nucleotide binding
K	0000502	cellular_component	proteasome complex
K	0005515	molecular_function	protein binding
K	0005524	molecular_function	ATP binding
K	0005634	cellular_component	nucleus
K	0005737	cellular_component	cytoplasm
K	0006511	biological_process	ubiquitin-dependent protein catabolic process
K	0008540	cellular_component	proteasome regulatory particle, base subcomplex
K	0010498	biological_process	proteasomal protein catabolic process
K	0010604	biological_process	positive regulation of macromolecule metabolic process
K	0016887	molecular_function	ATP hydrolysis activity
K	0036402	molecular_function	proteasome-activating activity
K	0042802	molecular_function	identical protein binding
K	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
K	0045899	biological_process	positive regulation of RNA polymerase II transcription preinitiation complex assembly
K	0070682	biological_process	proteasome regulatory particle assembly
K	0080090	biological_process	regulation of primary metabolic process
K	1901800	biological_process	positive regulation of proteasomal protein catabolic process
L	0000166	molecular_function	nucleotide binding
L	0000502	cellular_component	proteasome complex
L	0005515	molecular_function	protein binding
L	0005524	molecular_function	ATP binding
L	0005634	cellular_component	nucleus
L	0006289	biological_process	nucleotide-excision repair
L	0008540	cellular_component	proteasome regulatory particle, base subcomplex
L	0010498	biological_process	proteasomal protein catabolic process
L	0010604	biological_process	positive regulation of macromolecule metabolic process
L	0016887	molecular_function	ATP hydrolysis activity
L	0019904	molecular_function	protein domain specific binding
L	0031625	molecular_function	ubiquitin protein ligase binding
L	0032968	biological_process	positive regulation of transcription elongation by RNA polymerase II
L	0036402	molecular_function	proteasome-activating activity
L	0036503	biological_process	ERAD pathway
L	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
L	0045899	biological_process	positive regulation of RNA polymerase II transcription preinitiation complex assembly
L	0070682	biological_process	proteasome regulatory particle assembly
L	0080090	biological_process	regulation of primary metabolic process
L	1901800	biological_process	positive regulation of proteasomal protein catabolic process
M	0000166	molecular_function	nucleotide binding
M	0000502	cellular_component	proteasome complex
M	0005515	molecular_function	protein binding
M	0005524	molecular_function	ATP binding
M	0005634	cellular_component	nucleus
M	0005737	cellular_component	cytoplasm
M	0006511	biological_process	ubiquitin-dependent protein catabolic process
M	0008540	cellular_component	proteasome regulatory particle, base subcomplex
M	0010498	biological_process	proteasomal protein catabolic process
M	0010604	biological_process	positive regulation of macromolecule metabolic process
M	0016887	molecular_function	ATP hydrolysis activity
M	0036402	molecular_function	proteasome-activating activity
M	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
M	0045899	biological_process	positive regulation of RNA polymerase II transcription preinitiation complex assembly
M	0070682	biological_process	proteasome regulatory particle assembly
M	0080090	biological_process	regulation of primary metabolic process
M	1901800	biological_process	positive regulation of proteasomal protein catabolic process
r	0000266	biological_process	mitochondrial fission
r	0000502	cellular_component	proteasome complex
r	0004843	molecular_function	cysteine-type deubiquitinase activity
r	0005515	molecular_function	protein binding
r	0005634	cellular_component	nucleus
r	0005739	cellular_component	mitochondrion
r	0005829	cellular_component	cytosol
r	0006508	biological_process	proteolysis
r	0008233	molecular_function	peptidase activity
r	0008234	molecular_function	cysteine-type peptidase activity
r	0008237	molecular_function	metallopeptidase activity
r	0008270	molecular_function	zinc ion binding
r	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
r	0016559	biological_process	peroxisome fission
r	0016579	biological_process	protein deubiquitination
r	0016787	molecular_function	hydrolase activity
r	0034515	cellular_component	proteasome storage granule
r	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
r	0043248	biological_process	proteasome assembly
r	0046872	molecular_function	metal ion binding
r	0070628	molecular_function	proteasome binding
r	0140492	molecular_function	metal-dependent deubiquitinase activity
r	1902906	biological_process	proteasome storage granule assembly
u	0000027	biological_process	ribosomal large subunit assembly
u	0000055	biological_process	ribosomal large subunit export from nucleus
u	0002181	biological_process	cytoplasmic translation
u	0003735	molecular_function	structural constituent of ribosome
u	0005634	cellular_component	nucleus
u	0005737	cellular_component	cytoplasm
u	0005829	cellular_component	cytosol
u	0005840	cellular_component	ribosome
u	0006412	biological_process	translation
u	0008270	molecular_function	zinc ion binding
u	0016567	biological_process	protein ubiquitination
u	0019941	biological_process	modification-dependent protein catabolic process
u	0022625	cellular_component	cytosolic large ribosomal subunit
u	0031386	molecular_function	protein tag activity
u	0031625	molecular_function	ubiquitin protein ligase binding
u	0042254	biological_process	ribosome biogenesis
u	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	14
Details	binding site for residue ATP H 501

Chain	Residue
H	GLY212
H	HIS392
H	ARG420
I	LEU310
I	ARG340
I	ARG343
H	GLY253
H	THR254
H	GLY255
H	LYS256
H	THR257
H	LEU258
H	GLU310
H	ASN356

---

site_id	AC2
Number of Residues	15
Details	binding site for residue ATP I 501

Chain	Residue
I	ILE184
I	GLY186
I	GLY226
I	THR227
I	GLY228
I	LYS229
I	THR230
I	LEU231
I	ASP282
I	GLU283
I	ILE361
I	HIS365
I	ALA390
I	GLN393
J	ARG309

---

site_id	AC3
Number of Residues	12
Details	binding site for residue ATP J 501

Chain	Residue
J	MET149
J	GLY151
J	THR193
J	GLY194
J	LYS195
J	THR196
J	LEU197
J	ASN295
J	ILE327
J	HIS331
J	GLY355
J	ALA356

---

site_id	AC4
Number of Residues	10
Details	binding site for residue ADP K 501

Chain	Residue
K	GLY175
K	PRO215
K	GLY216
K	THR217
K	GLY218
K	LYS219
K	THR220
K	ASP272
K	ILE352
K	GLY380

---

site_id	AC5
Number of Residues	7
Details	binding site for residue ADP L 501

Chain	Residue
L	GLY184
L	THR226
L	GLY227
L	LYS228
L	THR229
L	HIS364
L	ALA389

---

site_id	AC6
Number of Residues	17
Details	binding site for residue ATP M 501

Chain	Residue
H	ARG367
H	ARG370
M	GLY184
M	PRO224
M	GLY225
M	THR226
M	GLY227
M	LYS228
M	THR229
M	LEU230
M	GLU282
M	ASN328
M	ILE360
M	HIS364
M	GLY388
M	ALA389
M	LYS392

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
u	LYS27-ASP52

---

site_id	PS00388
Number of Residues	23
Details	PROTEASOME_ALPHA_1 Proteasome alpha-type subunits signature. YdgdtVtFSPtGRlfQVEYAleA

Chain	Residue	Details
F	TYR6-ALA28
D	TYR4-ALA26
C	TYR6-SER28
E	TYR8-ALA30
G	TYR8-ALA30
A	TYR12-ALA34
B	TYR5-ALA27

---

site_id	PS00674
Number of Residues	19
Details	AAA AAA-protein family signature. IkIImATNrldiLDpALl.R

Chain	Residue	Details
J	ILE288-ARG306
I	VAL322-ARG340
H	ILE349-ARG367
K	VAL312-ARG330
L	THR321-ARG339
M	VAL321-ARG339

---

site_id	PS00854
Number of Residues	48
Details	PROTEASOME_BETA_1 Proteasome beta-type subunits signature. VGVkGknCVVLGCErrstlklqdtritps.KvskidshvvlsfsGlnAD

Chain	Residue	Details
D	VAL34-ASP81
C	ILE36-ASP83
7	ILE12-ASP59
1	MET4-ASP51
3	VAL13-ASP59
4	LEU5-ASP52
6	LEU13-ASP60
2	VAL4-ASP51
5	LEU4-ASP51

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
u	GLY76
r	HIS111
r	ASP122
C	LYS231

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047

Chain	Residue	Details
r	MET1
u	LYS93

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:19779198

Chain	Residue	Details
M	TYR180
I	LYS255
I	LYS290

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 177

Chain	Residue	Details
B	GLN30	covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
B	ALA46	activator, steric locator
B	GLU48	activator
B	SER62	activator, electrostatic stabiliser
B	SER76	electrostatic stabiliser
B	PRO158	activator, electrostatic stabiliser
B	THR195	activator, steric locator
B	GLU198	activator, electrostatic stabiliser

---