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8DAT

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to three ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intB)

Functional Information from GO Data
ChainGOidnamespacecontents
A0000837cellular_componentDoa10p ubiquitin ligase complex
A0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0005829cellular_componentcytosol
A0006274biological_processDNA replication termination
A0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
A0010636biological_processpositive regulation of mitochondrial fusion
A0015031biological_processprotein transport
A0016236biological_processmacroautophagy
A0016320biological_processendoplasmic reticulum membrane fusion
A0016787molecular_functionhydrolase activity
A0016887molecular_functionATP hydrolysis activity
A0019888molecular_functionprotein phosphatase regulator activity
A0030894cellular_componentreplisome
A0030970biological_processretrograde protein transport, ER to cytosol
A0031134biological_processsister chromatid biorientation
A0031593molecular_functionpolyubiquitin modification-dependent protein binding
A0032984biological_processprotein-containing complex disassembly
A0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
A0034517biological_processribophagy
A0034727biological_processpiecemeal microautophagy of the nucleus
A0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
A0036503biological_processERAD pathway
A0042802molecular_functionidentical protein binding
A0043130molecular_functionubiquitin binding
A0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
A0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
A0043332cellular_componentmating projection tip
A0046034biological_processATP metabolic process
A0051228biological_processmitotic spindle disassembly
A0070651biological_processnonfunctional rRNA decay
A0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
A0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
A0072344biological_processrescue of stalled ribosome
A0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
A0097352biological_processautophagosome maturation
A0099638biological_processendosome to plasma membrane protein transport
A0120174biological_processstress-induced homeostatically regulated protein degradation pathway
A1900182biological_processpositive regulation of protein localization to nucleus
A1902979biological_processmitotic DNA replication termination
A1990112cellular_componentRQC complex
A1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
A1990171biological_processSCF complex disassembly in response to cadmium stress
B0000837cellular_componentDoa10p ubiquitin ligase complex
B0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0005829cellular_componentcytosol
B0006274biological_processDNA replication termination
B0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
B0010636biological_processpositive regulation of mitochondrial fusion
B0015031biological_processprotein transport
B0016236biological_processmacroautophagy
B0016320biological_processendoplasmic reticulum membrane fusion
B0016787molecular_functionhydrolase activity
B0016887molecular_functionATP hydrolysis activity
B0019888molecular_functionprotein phosphatase regulator activity
B0030894cellular_componentreplisome
B0030970biological_processretrograde protein transport, ER to cytosol
B0031134biological_processsister chromatid biorientation
B0031593molecular_functionpolyubiquitin modification-dependent protein binding
B0032984biological_processprotein-containing complex disassembly
B0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
B0034517biological_processribophagy
B0034727biological_processpiecemeal microautophagy of the nucleus
B0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
B0036503biological_processERAD pathway
B0042802molecular_functionidentical protein binding
B0043130molecular_functionubiquitin binding
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
B0043332cellular_componentmating projection tip
B0046034biological_processATP metabolic process
B0051228biological_processmitotic spindle disassembly
B0070651biological_processnonfunctional rRNA decay
B0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
B0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
B0072344biological_processrescue of stalled ribosome
B0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
B0097352biological_processautophagosome maturation
B0099638biological_processendosome to plasma membrane protein transport
B0120174biological_processstress-induced homeostatically regulated protein degradation pathway
B1900182biological_processpositive regulation of protein localization to nucleus
B1902979biological_processmitotic DNA replication termination
B1990112cellular_componentRQC complex
B1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
B1990171biological_processSCF complex disassembly in response to cadmium stress
C0000837cellular_componentDoa10p ubiquitin ligase complex
C0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005739cellular_componentmitochondrion
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0005829cellular_componentcytosol
C0006274biological_processDNA replication termination
C0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
C0010636biological_processpositive regulation of mitochondrial fusion
C0015031biological_processprotein transport
C0016236biological_processmacroautophagy
C0016320biological_processendoplasmic reticulum membrane fusion
C0016787molecular_functionhydrolase activity
C0016887molecular_functionATP hydrolysis activity
C0019888molecular_functionprotein phosphatase regulator activity
C0030894cellular_componentreplisome
C0030970biological_processretrograde protein transport, ER to cytosol
C0031134biological_processsister chromatid biorientation
C0031593molecular_functionpolyubiquitin modification-dependent protein binding
C0032984biological_processprotein-containing complex disassembly
C0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
C0034517biological_processribophagy
C0034727biological_processpiecemeal microautophagy of the nucleus
C0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
C0036503biological_processERAD pathway
C0042802molecular_functionidentical protein binding
C0043130molecular_functionubiquitin binding
C0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
C0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
C0043332cellular_componentmating projection tip
C0046034biological_processATP metabolic process
C0051228biological_processmitotic spindle disassembly
C0070651biological_processnonfunctional rRNA decay
C0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
C0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
C0072344biological_processrescue of stalled ribosome
C0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
C0097352biological_processautophagosome maturation
C0099638biological_processendosome to plasma membrane protein transport
C0120174biological_processstress-induced homeostatically regulated protein degradation pathway
C1900182biological_processpositive regulation of protein localization to nucleus
C1902979biological_processmitotic DNA replication termination
C1990112cellular_componentRQC complex
C1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
C1990171biological_processSCF complex disassembly in response to cadmium stress
D0000837cellular_componentDoa10p ubiquitin ligase complex
D0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005739cellular_componentmitochondrion
D0005783cellular_componentendoplasmic reticulum
D0005789cellular_componentendoplasmic reticulum membrane
D0005829cellular_componentcytosol
D0006274biological_processDNA replication termination
D0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
D0010636biological_processpositive regulation of mitochondrial fusion
D0015031biological_processprotein transport
D0016236biological_processmacroautophagy
D0016320biological_processendoplasmic reticulum membrane fusion
D0016787molecular_functionhydrolase activity
D0016887molecular_functionATP hydrolysis activity
D0019888molecular_functionprotein phosphatase regulator activity
D0030894cellular_componentreplisome
D0030970biological_processretrograde protein transport, ER to cytosol
D0031134biological_processsister chromatid biorientation
D0031593molecular_functionpolyubiquitin modification-dependent protein binding
D0032984biological_processprotein-containing complex disassembly
D0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
D0034517biological_processribophagy
D0034727biological_processpiecemeal microautophagy of the nucleus
D0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
D0036503biological_processERAD pathway
D0042802molecular_functionidentical protein binding
D0043130molecular_functionubiquitin binding
D0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
D0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
D0043332cellular_componentmating projection tip
D0046034biological_processATP metabolic process
D0051228biological_processmitotic spindle disassembly
D0070651biological_processnonfunctional rRNA decay
D0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
D0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
D0072344biological_processrescue of stalled ribosome
D0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
D0097352biological_processautophagosome maturation
D0099638biological_processendosome to plasma membrane protein transport
D0120174biological_processstress-induced homeostatically regulated protein degradation pathway
D1900182biological_processpositive regulation of protein localization to nucleus
D1902979biological_processmitotic DNA replication termination
D1990112cellular_componentRQC complex
D1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
D1990171biological_processSCF complex disassembly in response to cadmium stress
E0000837cellular_componentDoa10p ubiquitin ligase complex
E0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
E0005515molecular_functionprotein binding
E0005524molecular_functionATP binding
E0005634cellular_componentnucleus
E0005737cellular_componentcytoplasm
E0005739cellular_componentmitochondrion
E0005783cellular_componentendoplasmic reticulum
E0005789cellular_componentendoplasmic reticulum membrane
E0005829cellular_componentcytosol
E0006274biological_processDNA replication termination
E0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
E0010636biological_processpositive regulation of mitochondrial fusion
E0015031biological_processprotein transport
E0016236biological_processmacroautophagy
E0016320biological_processendoplasmic reticulum membrane fusion
E0016787molecular_functionhydrolase activity
E0016887molecular_functionATP hydrolysis activity
E0019888molecular_functionprotein phosphatase regulator activity
E0030894cellular_componentreplisome
E0030970biological_processretrograde protein transport, ER to cytosol
E0031134biological_processsister chromatid biorientation
E0031593molecular_functionpolyubiquitin modification-dependent protein binding
E0032984biological_processprotein-containing complex disassembly
E0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
E0034517biological_processribophagy
E0034727biological_processpiecemeal microautophagy of the nucleus
E0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
E0036503biological_processERAD pathway
E0042802molecular_functionidentical protein binding
E0043130molecular_functionubiquitin binding
E0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
E0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
E0043332cellular_componentmating projection tip
E0046034biological_processATP metabolic process
E0051228biological_processmitotic spindle disassembly
E0070651biological_processnonfunctional rRNA decay
E0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
E0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
E0072344biological_processrescue of stalled ribosome
E0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
E0097352biological_processautophagosome maturation
E0099638biological_processendosome to plasma membrane protein transport
E0120174biological_processstress-induced homeostatically regulated protein degradation pathway
E1900182biological_processpositive regulation of protein localization to nucleus
E1902979biological_processmitotic DNA replication termination
E1990112cellular_componentRQC complex
E1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
E1990171biological_processSCF complex disassembly in response to cadmium stress
F0000837cellular_componentDoa10p ubiquitin ligase complex
F0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
F0005515molecular_functionprotein binding
F0005524molecular_functionATP binding
F0005634cellular_componentnucleus
F0005737cellular_componentcytoplasm
F0005739cellular_componentmitochondrion
F0005783cellular_componentendoplasmic reticulum
F0005789cellular_componentendoplasmic reticulum membrane
F0005829cellular_componentcytosol
F0006274biological_processDNA replication termination
F0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
F0010636biological_processpositive regulation of mitochondrial fusion
F0015031biological_processprotein transport
F0016236biological_processmacroautophagy
F0016320biological_processendoplasmic reticulum membrane fusion
F0016787molecular_functionhydrolase activity
F0016887molecular_functionATP hydrolysis activity
F0019888molecular_functionprotein phosphatase regulator activity
F0030894cellular_componentreplisome
F0030970biological_processretrograde protein transport, ER to cytosol
F0031134biological_processsister chromatid biorientation
F0031593molecular_functionpolyubiquitin modification-dependent protein binding
F0032984biological_processprotein-containing complex disassembly
F0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
F0034517biological_processribophagy
F0034727biological_processpiecemeal microautophagy of the nucleus
F0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
F0036503biological_processERAD pathway
F0042802molecular_functionidentical protein binding
F0043130molecular_functionubiquitin binding
F0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
F0043328biological_processprotein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
F0043332cellular_componentmating projection tip
F0046034biological_processATP metabolic process
F0051228biological_processmitotic spindle disassembly
F0070651biological_processnonfunctional rRNA decay
F0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
F0071630biological_processnuclear protein quality control by the ubiquitin-proteasome system
F0072344biological_processrescue of stalled ribosome
F0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
F0097352biological_processautophagosome maturation
F0099638biological_processendosome to plasma membrane protein transport
F0120174biological_processstress-induced homeostatically regulated protein degradation pathway
F1900182biological_processpositive regulation of protein localization to nucleus
F1902979biological_processmitotic DNA replication termination
F1990112cellular_componentRQC complex
F1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
F1990171biological_processSCF complex disassembly in response to cadmium stress
G0000837cellular_componentDoa10p ubiquitin ligase complex
G0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005737cellular_componentcytoplasm
G0005783cellular_componentendoplasmic reticulum
G0005789cellular_componentendoplasmic reticulum membrane
G0006274biological_processDNA replication termination
G0006511biological_processubiquitin-dependent protein catabolic process
G0006515biological_processprotein quality control for misfolded or incompletely synthesized proteins
G0008270molecular_functionzinc ion binding
G0015031biological_processprotein transport
G0016020cellular_componentmembrane
G0030894cellular_componentreplisome
G0030970biological_processretrograde protein transport, ER to cytosol
G0031625molecular_functionubiquitin protein ligase binding
G0031965cellular_componentnuclear membrane
G0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
G0036266cellular_componentCdc48p-Npl4p-Vms1p AAA ATPase complex
G0036435molecular_functionK48-linked polyubiquitin modification-dependent protein binding
G0036503biological_processERAD pathway
G0042175cellular_componentnuclear outer membrane-endoplasmic reticulum membrane network
G0043130molecular_functionubiquitin binding
G0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
G0048471cellular_componentperinuclear region of cytoplasm
G0051028biological_processmRNA transport
G0051228biological_processmitotic spindle disassembly
G0070651biological_processnonfunctional rRNA decay
G0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
G0072344biological_processrescue of stalled ribosome
G0072665biological_processprotein localization to vacuole
G0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
G0099638biological_processendosome to plasma membrane protein transport
G1900182biological_processpositive regulation of protein localization to nucleus
G1990112cellular_componentRQC complex
G1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
H0000837cellular_componentDoa10p ubiquitin ligase complex
H0000839cellular_componentHrd1p ubiquitin ligase ERAD-L complex
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005829cellular_componentcytosol
H0006274biological_processDNA replication termination
H0006511biological_processubiquitin-dependent protein catabolic process
H0030894cellular_componentreplisome
H0030970biological_processretrograde protein transport, ER to cytosol
H0031593molecular_functionpolyubiquitin modification-dependent protein binding
H0034098cellular_componentVCP-NPL4-UFD1 AAA ATPase complex
H0036503biological_processERAD pathway
H0043130molecular_functionubiquitin binding
H0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
H0070651biological_processnonfunctional rRNA decay
H0071629biological_processcytoplasm protein quality control by the ubiquitin-proteasome system
H0072344biological_processrescue of stalled ribosome
H0072665biological_processprotein localization to vacuole
H0072671biological_processmitochondria-associated ubiquitin-dependent protein catabolic process
H1900182biological_processpositive regulation of protein localization to nucleus
H1990112cellular_componentRQC complex
H1990116biological_processribosome-associated ubiquitin-dependent protein catabolic process
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KskIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
JLYS127-ASP152

site_idPS00430
Number of Residues75
DetailsTONB_DEPENDENT_REC_1 TonB-dependent receptor (TBDR) proteins signature 1. gshmgeehkplldasgvdpreedktatailrrkkkdnmllvddainddnsviainsntmdklelfrg................................................DTVLVKGK
ChainResidueDetails
AGLY-2-LYS72

site_idPS00674
Number of Residues19
DetailsAAA AAA-protein family signature. VvVIaATNrpnsIDpALr.R
ChainResidueDetails
AVAL351-ARG369
AVAL627-ARG645

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues18
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0CG47
ChainResidueDetails
JLYS106
KLYS229
KLYS233
KLYS263
LLYS306
LLYS311
LLYS327
LLYS329
LLYS333
LLYS363
JLYS111
JLYS127
JLYS129
JLYS133
JLYS163
KLYS206
KLYS211
KLYS227

site_idSWS_FT_FI2
Number of Residues6
DetailsCROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) => ECO:0000255|PROSITE-ProRule:PRU00214
ChainResidueDetails
HSER354
JGLY176
CGLY531
KGLY276
EGLY531
LGLY376

site_idSWS_FT_FI3
Number of Residues3
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:7862120
ChainResidueDetails
JLYS148
KLYS248
LLYS348
DSER472
ESER472
FSER472

site_idSWS_FT_FI4
Number of Residues6
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:19779198
ChainResidueDetails
ASER519
BSER519
CSER519
DSER519
ESER519
FSER519

site_idSWS_FT_FI5
Number of Residues6
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198
ChainResidueDetails
ATHR735
BTHR735
CTHR735
DTHR735
ETHR735
FTHR735

site_idSWS_FT_FI6
Number of Residues6
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17287358, ECO:0007744|PubMed:17330950
ChainResidueDetails
ASER770
BSER770
CSER770
DSER770
ESER770
FSER770

site_idSWS_FT_FI7
Number of Residues30
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047
ChainResidueDetails
ALYS305
BLYS539
CLYS305
CLYS322
CLYS346
CLYS522
CLYS539
DLYS305
DLYS322
DLYS346
DLYS522
ALYS322
DLYS539
ELYS305
ELYS322
ELYS346
ELYS522
ELYS539
FLYS305
FLYS322
FLYS346
FLYS522
ALYS346
FLYS539
ALYS522
ALYS539
BLYS305
BLYS322
BLYS346
BLYS522

site_idSWS_FT_FI8
Number of Residues18
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:12872131
ChainResidueDetails
DLYS594
DLYS673
ELYS594
ELYS673
FLYS594
FLYS673
ALYS594
ALYS673
BLYS594
BLYS673
CLYS594
CLYS673

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PDB entries from 2024-07-24

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