9U4M

Focused refinement of 19S in the substrate-engaged human 26S proteasome bound to midnolin with RPT6 at top of spiral staircase

Functional Information from GO Data

Chain	GOid	namespace	contents
a	0000502	cellular_component	proteasome complex
a	0005198	molecular_function	structural molecule activity
a	0005515	molecular_function	protein binding
a	0005576	cellular_component	extracellular region
a	0005634	cellular_component	nucleus
a	0005654	cellular_component	nucleoplasm
a	0005829	cellular_component	cytosol
a	0005838	cellular_component	proteasome regulatory particle
a	0006511	biological_process	ubiquitin-dependent protein catabolic process
a	0006979	biological_process	response to oxidative stress
a	0008021	cellular_component	synaptic vesicle
a	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
a	0010498	biological_process	proteasomal protein catabolic process
a	0016020	cellular_component	membrane
a	0022624	cellular_component	proteasome accessory complex
a	0034774	cellular_component	secretory granule lumen
a	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
a	0061136	biological_process	regulation of proteasomal protein catabolic process
a	0071357	biological_process	cellular response to type I interferon
a	1904813	cellular_component	ficolin-1-rich granule lumen
A	0000502	cellular_component	proteasome complex
A	0000932	cellular_component	P-body
A	0001649	biological_process	osteoblast differentiation
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006979	biological_process	response to oxidative stress
A	0008021	cellular_component	synaptic vesicle
A	0010498	biological_process	proteasomal protein catabolic process
A	0016020	cellular_component	membrane
A	0022624	cellular_component	proteasome accessory complex
A	0034774	cellular_component	secretory granule lumen
A	0036402	molecular_function	proteasome-activating activity
A	0036464	cellular_component	cytoplasmic ribonucleoprotein granule
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0061136	biological_process	regulation of proteasomal protein catabolic process
A	0071357	biological_process	cellular response to type I interferon
A	1901800	biological_process	positive regulation of proteasomal protein catabolic process
A	1904813	cellular_component	ficolin-1-rich granule lumen
b	0000502	cellular_component	proteasome complex
b	0003723	molecular_function	RNA binding
b	0005515	molecular_function	protein binding
b	0005634	cellular_component	nucleus
b	0005829	cellular_component	cytosol
b	0006979	biological_process	response to oxidative stress
b	0008021	cellular_component	synaptic vesicle
b	0010498	biological_process	proteasomal protein catabolic process
b	0022624	cellular_component	proteasome accessory complex
b	0042802	molecular_function	identical protein binding
b	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
b	0060090	molecular_function	molecular adaptor activity
b	0061136	biological_process	regulation of proteasomal protein catabolic process
b	0071357	biological_process	cellular response to type I interferon
B	0000502	cellular_component	proteasome complex
B	0003723	molecular_function	RNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005838	cellular_component	proteasome regulatory particle
B	0006979	biological_process	response to oxidative stress
B	0008021	cellular_component	synaptic vesicle
B	0010498	biological_process	proteasomal protein catabolic process
B	0016020	cellular_component	membrane
B	0022624	cellular_component	proteasome accessory complex
B	0036402	molecular_function	proteasome-activating activity
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0061136	biological_process	regulation of proteasomal protein catabolic process
B	0071357	biological_process	cellular response to type I interferon
c	0000502	cellular_component	proteasome complex
c	0000724	biological_process	double-strand break repair via homologous recombination
c	0004843	molecular_function	cysteine-type deubiquitinase activity
c	0005515	molecular_function	protein binding
c	0005576	cellular_component	extracellular region
c	0005634	cellular_component	nucleus
c	0005654	cellular_component	nucleoplasm
c	0005829	cellular_component	cytosol
c	0006303	biological_process	double-strand break repair via nonhomologous end joining
c	0006511	biological_process	ubiquitin-dependent protein catabolic process
c	0006890	biological_process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
c	0006979	biological_process	response to oxidative stress
c	0008021	cellular_component	synaptic vesicle
c	0008237	molecular_function	metallopeptidase activity
c	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
c	0010498	biological_process	proteasomal protein catabolic process
c	0016241	biological_process	regulation of macroautophagy
c	0016579	biological_process	protein deubiquitination
c	0022624	cellular_component	proteasome accessory complex
c	0031597	cellular_component	cytosolic proteasome complex
c	0034774	cellular_component	secretory granule lumen
c	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
c	0045471	biological_process	response to ethanol
c	0061133	molecular_function	endopeptidase activator activity
c	0061136	biological_process	regulation of proteasomal protein catabolic process
c	0061578	molecular_function	K63-linked deubiquitinase activity
c	0070536	biological_process	protein K63-linked deubiquitination
c	0070628	molecular_function	proteasome binding
c	0071357	biological_process	cellular response to type I interferon
c	0140492	molecular_function	metal-dependent deubiquitinase activity
c	1904813	cellular_component	ficolin-1-rich granule lumen
C	0000502	cellular_component	proteasome complex
C	0005102	molecular_function	signaling receptor binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005838	cellular_component	proteasome regulatory particle
C	0005886	cellular_component	plasma membrane
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0006979	biological_process	response to oxidative stress
C	0008021	cellular_component	synaptic vesicle
C	0008134	molecular_function	transcription factor binding
C	0010498	biological_process	proteasomal protein catabolic process
C	0016020	cellular_component	membrane
C	0016234	cellular_component	inclusion body
C	0016887	molecular_function	ATP hydrolysis activity
C	0017025	molecular_function	TBP-class protein binding
C	0022624	cellular_component	proteasome accessory complex
C	0031410	cellular_component	cytoplasmic vesicle
C	0031531	molecular_function	thyrotropin-releasing hormone receptor binding
C	0031595	cellular_component	nuclear proteasome complex
C	0031597	cellular_component	cytosolic proteasome complex
C	0036402	molecular_function	proteasome-activating activity
C	0043069	biological_process	negative regulation of programmed cell death
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0045893	biological_process	positive regulation of DNA-templated transcription
C	0061136	biological_process	regulation of proteasomal protein catabolic process
C	0070062	cellular_component	extracellular exosome
C	0071357	biological_process	cellular response to type I interferon
C	0072562	cellular_component	blood microparticle
C	0090261	biological_process	positive regulation of inclusion body assembly
C	0140296	molecular_function	general transcription initiation factor binding
C	0140297	molecular_function	DNA-binding transcription factor binding
C	1901800	biological_process	positive regulation of proteasomal protein catabolic process
d	0000502	cellular_component	proteasome complex
d	0005515	molecular_function	protein binding
d	0005634	cellular_component	nucleus
d	0005654	cellular_component	nucleoplasm
d	0005829	cellular_component	cytosol
d	0005838	cellular_component	proteasome regulatory particle
d	0006979	biological_process	response to oxidative stress
d	0008021	cellular_component	synaptic vesicle
d	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
d	0010498	biological_process	proteasomal protein catabolic process
d	0022624	cellular_component	proteasome accessory complex
d	0032991	cellular_component	protein-containing complex
d	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
d	0061136	biological_process	regulation of proteasomal protein catabolic process
d	0071357	biological_process	cellular response to type I interferon
D	0000502	cellular_component	proteasome complex
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006508	biological_process	proteolysis
D	0006979	biological_process	response to oxidative stress
D	0008021	cellular_component	synaptic vesicle
D	0010498	biological_process	proteasomal protein catabolic process
D	0016020	cellular_component	membrane
D	0022624	cellular_component	proteasome accessory complex
D	0036402	molecular_function	proteasome-activating activity
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0061136	biological_process	regulation of proteasomal protein catabolic process
D	0071357	biological_process	cellular response to type I interferon
e	0000502	cellular_component	proteasome complex
e	0005515	molecular_function	protein binding
e	0005634	cellular_component	nucleus
e	0005654	cellular_component	nucleoplasm
e	0005829	cellular_component	cytosol
e	0006406	biological_process	mRNA export from nucleus
e	0006979	biological_process	response to oxidative stress
e	0008021	cellular_component	synaptic vesicle
e	0010498	biological_process	proteasomal protein catabolic process
e	0032039	cellular_component	integrator complex
e	0032991	cellular_component	protein-containing complex
e	0043130	molecular_function	ubiquitin binding
e	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
e	0045944	biological_process	positive regulation of transcription by RNA polymerase II
e	0061136	biological_process	regulation of proteasomal protein catabolic process
e	0070390	cellular_component	transcription export complex 2
e	0071357	biological_process	cellular response to type I interferon
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
F	0000502	cellular_component	proteasome complex
F	0000932	cellular_component	P-body
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006979	biological_process	response to oxidative stress
F	0008021	cellular_component	synaptic vesicle
F	0010498	biological_process	proteasomal protein catabolic process
F	0016020	cellular_component	membrane
F	0022624	cellular_component	proteasome accessory complex
F	0034774	cellular_component	secretory granule lumen
F	0036402	molecular_function	proteasome-activating activity
F	0042802	molecular_function	identical protein binding
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0043921	biological_process	host-mediated perturbation of viral transcription
F	0045944	biological_process	positive regulation of transcription by RNA polymerase II
F	0061136	biological_process	regulation of proteasomal protein catabolic process
F	0071357	biological_process	cellular response to type I interferon
F	1901800	biological_process	positive regulation of proteasomal protein catabolic process
F	1904813	cellular_component	ficolin-1-rich granule lumen
U	0000502	cellular_component	proteasome complex
U	0005515	molecular_function	protein binding
U	0005576	cellular_component	extracellular region
U	0005654	cellular_component	nucleoplasm
U	0005829	cellular_component	cytosol
U	0005838	cellular_component	proteasome regulatory particle
U	0006979	biological_process	response to oxidative stress
U	0008021	cellular_component	synaptic vesicle
U	0010498	biological_process	proteasomal protein catabolic process
U	0016020	cellular_component	membrane
U	0022624	cellular_component	proteasome accessory complex
U	0031625	molecular_function	ubiquitin protein ligase binding
U	0034515	cellular_component	proteasome storage granule
U	0035578	cellular_component	azurophil granule lumen
U	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
U	0061136	biological_process	regulation of proteasomal protein catabolic process
U	0071357	biological_process	cellular response to type I interferon
V	0000502	cellular_component	proteasome complex
V	0005515	molecular_function	protein binding
V	0005576	cellular_component	extracellular region
V	0005634	cellular_component	nucleus
V	0005654	cellular_component	nucleoplasm
V	0005829	cellular_component	cytosol
V	0005838	cellular_component	proteasome regulatory particle
V	0006511	biological_process	ubiquitin-dependent protein catabolic process
V	0006979	biological_process	response to oxidative stress
V	0008021	cellular_component	synaptic vesicle
V	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
V	0010498	biological_process	proteasomal protein catabolic process
V	0016020	cellular_component	membrane
V	0022624	cellular_component	proteasome accessory complex
V	0034774	cellular_component	secretory granule lumen
V	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
V	0061136	biological_process	regulation of proteasomal protein catabolic process
V	0070062	cellular_component	extracellular exosome
V	0071357	biological_process	cellular response to type I interferon
V	1904813	cellular_component	ficolin-1-rich granule lumen
W	0000502	cellular_component	proteasome complex
W	0005515	molecular_function	protein binding
W	0005576	cellular_component	extracellular region
W	0005654	cellular_component	nucleoplasm
W	0005829	cellular_component	cytosol
W	0005838	cellular_component	proteasome regulatory particle
W	0006979	biological_process	response to oxidative stress
W	0008021	cellular_component	synaptic vesicle
W	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
W	0010498	biological_process	proteasomal protein catabolic process
W	0016020	cellular_component	membrane
W	0022624	cellular_component	proteasome accessory complex
W	0034774	cellular_component	secretory granule lumen
W	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
W	0061136	biological_process	regulation of proteasomal protein catabolic process
W	0070062	cellular_component	extracellular exosome
W	0071357	biological_process	cellular response to type I interferon
W	1904813	cellular_component	ficolin-1-rich granule lumen
X	0000502	cellular_component	proteasome complex
X	0005198	molecular_function	structural molecule activity
X	0005515	molecular_function	protein binding
X	0005576	cellular_component	extracellular region
X	0005634	cellular_component	nucleus
X	0005654	cellular_component	nucleoplasm
X	0005829	cellular_component	cytosol
X	0005838	cellular_component	proteasome regulatory particle
X	0006511	biological_process	ubiquitin-dependent protein catabolic process
X	0006979	biological_process	response to oxidative stress
X	0008021	cellular_component	synaptic vesicle
X	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
X	0010498	biological_process	proteasomal protein catabolic process
X	0016020	cellular_component	membrane
X	0022624	cellular_component	proteasome accessory complex
X	0032991	cellular_component	protein-containing complex
X	0034774	cellular_component	secretory granule lumen
X	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
X	0043248	biological_process	proteasome assembly
X	0048863	biological_process	stem cell differentiation
X	0061136	biological_process	regulation of proteasomal protein catabolic process
X	0071357	biological_process	cellular response to type I interferon
X	1904813	cellular_component	ficolin-1-rich granule lumen
Y	0000502	cellular_component	proteasome complex
Y	0005515	molecular_function	protein binding
Y	0005576	cellular_component	extracellular region
Y	0005654	cellular_component	nucleoplasm
Y	0005829	cellular_component	cytosol
Y	0005838	cellular_component	proteasome regulatory particle
Y	0006979	biological_process	response to oxidative stress
Y	0008021	cellular_component	synaptic vesicle
Y	0010498	biological_process	proteasomal protein catabolic process
Y	0022624	cellular_component	proteasome accessory complex
Y	0032991	cellular_component	protein-containing complex
Y	0034774	cellular_component	secretory granule lumen
Y	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
Y	0061136	biological_process	regulation of proteasomal protein catabolic process
Y	0071357	biological_process	cellular response to type I interferon
Y	1904813	cellular_component	ficolin-1-rich granule lumen
Z	0000502	cellular_component	proteasome complex
Z	0005515	molecular_function	protein binding
Z	0005576	cellular_component	extracellular region
Z	0005634	cellular_component	nucleus
Z	0005654	cellular_component	nucleoplasm
Z	0005829	cellular_component	cytosol
Z	0005838	cellular_component	proteasome regulatory particle
Z	0006979	biological_process	response to oxidative stress
Z	0008021	cellular_component	synaptic vesicle
Z	0008233	molecular_function	peptidase activity
Z	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
Z	0010498	biological_process	proteasomal protein catabolic process
Z	0016020	cellular_component	membrane
Z	0034774	cellular_component	secretory granule lumen
Z	0042803	molecular_function	protein homodimerization activity
Z	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
Z	0061136	biological_process	regulation of proteasomal protein catabolic process
Z	0070062	cellular_component	extracellular exosome
Z	0071357	biological_process	cellular response to type I interferon
Z	0140492	molecular_function	metal-dependent deubiquitinase activity
Z	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PROSITE/UniProt

site_id	PS00012
Number of Residues	16
Details	PHOSPHOPANTETHEINE Phosphopantetheine attachment site. AAGFSSSGPAATSGAV

Chain	Residue	Details
d	ALA72-VAL87

---

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

Chain	Residue	Details
D	VAL305-ARG323
B	VAL325-ARG343
C	ILE289-ARG307
F	VAL326-ARG344
E	VAL273-ARG291
A	ILE315-ARG333

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1029
Details	Domain: {"description":"PCI","evidences":[{"source":"PROSITE-ProRule","id":"PRU01185","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	11
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	35
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"17370265","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	13
Details	Motif: {"description":"JAMM motif","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17693683","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17323924","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","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)"}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	33
Details	Repeat: {"description":"PC 2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	34
Details	Repeat: {"description":"PC 3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	34
Details	Repeat: {"description":"PC 4"}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	33
Details	Repeat: {"description":"PC 5"}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	35
Details	Repeat: {"description":"PC 6"}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	32
Details	Repeat: {"description":"PC 7"}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	34
Details	Repeat: {"description":"PC 8"}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	40
Details	Repeat: {"description":"PC 9"}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	32
Details	Repeat: {"description":"PC 10"}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q3TXS7","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"25114211","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25218447","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25772364","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	5
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI32
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"25772364","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI33
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI34
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---