5VHS

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005524	molecular_function	ATP binding
A	0016887	molecular_function	ATP hydrolysis activity
B	0005524	molecular_function	ATP binding
B	0016887	molecular_function	ATP hydrolysis activity
C	0000166	molecular_function	nucleotide binding
C	0000502	cellular_component	proteasome complex
C	0005102	molecular_function	signaling receptor binding
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP 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	0008540	cellular_component	proteasome regulatory particle, base subcomplex
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	0005524	molecular_function	ATP binding
D	0016887	molecular_function	ATP hydrolysis activity
E	0000166	molecular_function	nucleotide binding
E	0000502	cellular_component	proteasome complex
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006979	biological_process	response to oxidative stress
E	0008021	cellular_component	synaptic vesicle
E	0008540	cellular_component	proteasome regulatory particle, base subcomplex
E	0010498	biological_process	proteasomal protein catabolic process
E	0016020	cellular_component	membrane
E	0016234	cellular_component	inclusion body
E	0016887	molecular_function	ATP hydrolysis activity
E	0022624	cellular_component	proteasome accessory complex
E	0030674	molecular_function	protein-macromolecule adaptor activity
E	0031597	cellular_component	cytosolic proteasome complex
E	0036402	molecular_function	proteasome-activating activity
E	0036503	biological_process	ERAD pathway
E	0042802	molecular_function	identical protein binding
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0045899	biological_process	positive regulation of RNA polymerase II transcription preinitiation complex assembly
E	0061136	biological_process	regulation of proteasomal protein catabolic process
E	0070062	cellular_component	extracellular exosome
E	0071357	biological_process	cellular response to type I interferon
E	0090261	biological_process	positive regulation of inclusion body assembly
E	1901800	biological_process	positive regulation of proteasomal protein catabolic process
F	0005524	molecular_function	ATP binding
F	0016887	molecular_function	ATP hydrolysis activity
U	0000502	cellular_component	proteasome complex
U	0005515	molecular_function	protein binding
U	0005576	cellular_component	extracellular region
U	0005634	cellular_component	nucleus
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	0008540	cellular_component	proteasome regulatory particle, base subcomplex
U	0010498	biological_process	proteasomal protein catabolic process
U	0016020	cellular_component	membrane
U	0022624	cellular_component	proteasome accessory complex
U	0030234	molecular_function	enzyme regulator activity
U	0031625	molecular_function	ubiquitin protein ligase binding
U	0034515	cellular_component	proteasome storage granule
U	0035578	cellular_component	azurophil granule lumen
U	0042176	biological_process	regulation of protein catabolic process
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	0030234	molecular_function	enzyme regulator activity
V	0034774	cellular_component	secretory granule lumen
V	0042176	biological_process	regulation of protein catabolic process
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	0005737	cellular_component	cytoplasm
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	0005838	cellular_component	proteasome regulatory particle
Z	0008233	molecular_function	peptidase activity
Z	0008237	molecular_function	metallopeptidase activity
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
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	0006281	biological_process	DNA repair
c	0006303	biological_process	double-strand break repair via nonhomologous end joining
c	0006508	biological_process	proteolysis
c	0006511	biological_process	ubiquitin-dependent protein catabolic process
c	0006890	biological_process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
c	0006914	biological_process	autophagy
c	0006974	biological_process	DNA damage response
c	0006979	biological_process	response to oxidative stress
c	0008021	cellular_component	synaptic vesicle
c	0008233	molecular_function	peptidase activity
c	0008234	molecular_function	cysteine-type peptidase activity
c	0008237	molecular_function	metallopeptidase activity
c	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
c	0010498	biological_process	proteasomal protein catabolic process
c	0016192	biological_process	vesicle-mediated transport
c	0016241	biological_process	regulation of macroautophagy
c	0016579	biological_process	protein deubiquitination
c	0016787	molecular_function	hydrolase activity
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	0046872	molecular_function	metal ion binding
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
d	0005838	cellular_component	proteasome regulatory particle
d	0006508	biological_process	proteolysis
e	0006406	biological_process	mRNA export from nucleus
e	0008541	cellular_component	proteasome regulatory particle, lid subcomplex
e	0043248	biological_process	proteasome assembly
f	0000502	cellular_component	proteasome complex
f	0030234	molecular_function	enzyme regulator activity
f	0042176	biological_process	regulation of protein catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	binding site for residue ZN c 400

Chain	Residue
c	PHE118

---

Functional Information from PROSITE/UniProt

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

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

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	42
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	13
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	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_FI4
Number of Residues	5
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	66
Details	Repeat: {"description":"PC 1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	69
Details	Repeat: {"description":"PC 2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	34
Details	Repeat: {"description":"PC 3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	68
Details	Repeat: {"description":"PC 4"}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	62
Details	Repeat: {"description":"PC 5"}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	35
Details	Repeat: {"description":"PC 6"}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	32
Details	Repeat: {"description":"PC 7"}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	34
Details	Repeat: {"description":"PC 8"}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	40
Details	Repeat: {"description":"PC 9"}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	32
Details	Repeat: {"description":"PC 10"}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"17323924","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
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_FI17
Number of Residues	860
Details	Domain: {"description":"PCI","evidences":[{"source":"PROSITE-ProRule","id":"PRU01185","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
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_FI19
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_FI20
Number of Residues	270
Details	Domain: {"description":"MPN","evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

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 ubiquitin)"}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	183
Details	Domain: {"description":"VWFA","evidences":[{"source":"PROSITE-ProRule","id":"PRU00219","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
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

---

site_id	SWS_FT_FI24
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_FI25
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01182","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI26
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_FI27
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17323924","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI28
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI29
Number of Residues	22
Details	Region: {"description":"Disordered","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI30
Number of Residues	20
Details	Compositional bias: {"description":"Basic and acidic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI31
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI32
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI33
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q8VDM4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---