Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6OAA

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000166	molecular_function	nucleotide binding
B	0000837	cellular_component	Doa10p ubiquitin ligase complex
B	0000839	cellular_component	Hrd1p ubiquitin ligase ERAD-L complex
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005783	cellular_component	endoplasmic reticulum
B	0005789	cellular_component	endoplasmic reticulum membrane
B	0005829	cellular_component	cytosol
B	0006274	biological_process	DNA replication termination
B	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
B	0007049	biological_process	cell cycle
B	0010636	biological_process	positive regulation of mitochondrial fusion
B	0015031	biological_process	protein transport
B	0016236	biological_process	macroautophagy
B	0016320	biological_process	endoplasmic reticulum membrane fusion
B	0016787	molecular_function	hydrolase activity
B	0016887	molecular_function	ATP hydrolysis activity
B	0019888	molecular_function	protein phosphatase regulator activity
B	0030894	cellular_component	replisome
B	0030970	biological_process	retrograde protein transport, ER to cytosol
B	0031134	biological_process	sister chromatid biorientation
B	0031593	molecular_function	polyubiquitin modification-dependent protein binding
B	0032984	biological_process	protein-containing complex disassembly
B	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
B	0034517	biological_process	ribophagy
B	0034727	biological_process	piecemeal microautophagy of the nucleus
B	0036266	cellular_component	Cdc48p-Npl4p-Vms1p AAA ATPase complex
B	0036503	biological_process	ERAD pathway
B	0042802	molecular_function	identical protein binding
B	0043130	molecular_function	ubiquitin binding
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0043231	cellular_component	intracellular membrane-bounded organelle
B	0043328	biological_process	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
B	0043332	cellular_component	mating projection tip
B	0046034	biological_process	ATP metabolic process
B	0050896	biological_process	response to stimulus
B	0051228	biological_process	mitotic spindle disassembly
B	0070651	biological_process	nonfunctional rRNA decay
B	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
B	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
B	0072344	biological_process	rescue of stalled ribosome
B	0072671	biological_process	mitochondria-associated ubiquitin-dependent protein catabolic process
B	0097352	biological_process	autophagosome maturation
B	0120174	biological_process	stress-induced homeostatically regulated protein degradation pathway
B	1900182	biological_process	positive regulation of protein localization to nucleus
B	1990112	cellular_component	RQC complex
B	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
B	1990171	biological_process	SCF complex disassembly in response to cadmium stress
C	0000166	molecular_function	nucleotide binding
C	0000837	cellular_component	Doa10p ubiquitin ligase complex
C	0000839	cellular_component	Hrd1p ubiquitin ligase ERAD-L complex
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005783	cellular_component	endoplasmic reticulum
C	0005789	cellular_component	endoplasmic reticulum membrane
C	0005829	cellular_component	cytosol
C	0006274	biological_process	DNA replication termination
C	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
C	0007049	biological_process	cell cycle
C	0010636	biological_process	positive regulation of mitochondrial fusion
C	0015031	biological_process	protein transport
C	0016236	biological_process	macroautophagy
C	0016320	biological_process	endoplasmic reticulum membrane fusion
C	0016787	molecular_function	hydrolase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0019888	molecular_function	protein phosphatase regulator activity
C	0030894	cellular_component	replisome
C	0030970	biological_process	retrograde protein transport, ER to cytosol
C	0031134	biological_process	sister chromatid biorientation
C	0031593	molecular_function	polyubiquitin modification-dependent protein binding
C	0032984	biological_process	protein-containing complex disassembly
C	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
C	0034517	biological_process	ribophagy
C	0034727	biological_process	piecemeal microautophagy of the nucleus
C	0036266	cellular_component	Cdc48p-Npl4p-Vms1p AAA ATPase complex
C	0036503	biological_process	ERAD pathway
C	0042802	molecular_function	identical protein binding
C	0043130	molecular_function	ubiquitin binding
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0043231	cellular_component	intracellular membrane-bounded organelle
C	0043328	biological_process	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
C	0043332	cellular_component	mating projection tip
C	0046034	biological_process	ATP metabolic process
C	0050896	biological_process	response to stimulus
C	0051228	biological_process	mitotic spindle disassembly
C	0070651	biological_process	nonfunctional rRNA decay
C	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
C	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
C	0072344	biological_process	rescue of stalled ribosome
C	0072671	biological_process	mitochondria-associated ubiquitin-dependent protein catabolic process
C	0097352	biological_process	autophagosome maturation
C	0120174	biological_process	stress-induced homeostatically regulated protein degradation pathway
C	1900182	biological_process	positive regulation of protein localization to nucleus
C	1990112	cellular_component	RQC complex
C	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
C	1990171	biological_process	SCF complex disassembly in response to cadmium stress
D	0000166	molecular_function	nucleotide binding
D	0000837	cellular_component	Doa10p ubiquitin ligase complex
D	0000839	cellular_component	Hrd1p ubiquitin ligase ERAD-L complex
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005783	cellular_component	endoplasmic reticulum
D	0005789	cellular_component	endoplasmic reticulum membrane
D	0005829	cellular_component	cytosol
D	0006274	biological_process	DNA replication termination
D	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
D	0007049	biological_process	cell cycle
D	0010636	biological_process	positive regulation of mitochondrial fusion
D	0015031	biological_process	protein transport
D	0016236	biological_process	macroautophagy
D	0016320	biological_process	endoplasmic reticulum membrane fusion
D	0016787	molecular_function	hydrolase activity
D	0016887	molecular_function	ATP hydrolysis activity
D	0019888	molecular_function	protein phosphatase regulator activity
D	0030894	cellular_component	replisome
D	0030970	biological_process	retrograde protein transport, ER to cytosol
D	0031134	biological_process	sister chromatid biorientation
D	0031593	molecular_function	polyubiquitin modification-dependent protein binding
D	0032984	biological_process	protein-containing complex disassembly
D	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
D	0034517	biological_process	ribophagy
D	0034727	biological_process	piecemeal microautophagy of the nucleus
D	0036266	cellular_component	Cdc48p-Npl4p-Vms1p AAA ATPase complex
D	0036503	biological_process	ERAD pathway
D	0042802	molecular_function	identical protein binding
D	0043130	molecular_function	ubiquitin binding
D	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
D	0043231	cellular_component	intracellular membrane-bounded organelle
D	0043328	biological_process	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
D	0043332	cellular_component	mating projection tip
D	0046034	biological_process	ATP metabolic process
D	0050896	biological_process	response to stimulus
D	0051228	biological_process	mitotic spindle disassembly
D	0070651	biological_process	nonfunctional rRNA decay
D	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
D	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
D	0072344	biological_process	rescue of stalled ribosome
D	0072671	biological_process	mitochondria-associated ubiquitin-dependent protein catabolic process
D	0097352	biological_process	autophagosome maturation
D	0120174	biological_process	stress-induced homeostatically regulated protein degradation pathway
D	1900182	biological_process	positive regulation of protein localization to nucleus
D	1990112	cellular_component	RQC complex
D	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
D	1990171	biological_process	SCF complex disassembly in response to cadmium stress
E	0000166	molecular_function	nucleotide binding
E	0000837	cellular_component	Doa10p ubiquitin ligase complex
E	0000839	cellular_component	Hrd1p ubiquitin ligase ERAD-L complex
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005783	cellular_component	endoplasmic reticulum
E	0005789	cellular_component	endoplasmic reticulum membrane
E	0005829	cellular_component	cytosol
E	0006274	biological_process	DNA replication termination
E	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
E	0007049	biological_process	cell cycle
E	0010636	biological_process	positive regulation of mitochondrial fusion
E	0015031	biological_process	protein transport
E	0016236	biological_process	macroautophagy
E	0016320	biological_process	endoplasmic reticulum membrane fusion
E	0016787	molecular_function	hydrolase activity
E	0016887	molecular_function	ATP hydrolysis activity
E	0019888	molecular_function	protein phosphatase regulator activity
E	0030894	cellular_component	replisome
E	0030970	biological_process	retrograde protein transport, ER to cytosol
E	0031134	biological_process	sister chromatid biorientation
E	0031593	molecular_function	polyubiquitin modification-dependent protein binding
E	0032984	biological_process	protein-containing complex disassembly
E	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
E	0034517	biological_process	ribophagy
E	0034727	biological_process	piecemeal microautophagy of the nucleus
E	0036266	cellular_component	Cdc48p-Npl4p-Vms1p AAA ATPase complex
E	0036503	biological_process	ERAD pathway
E	0042802	molecular_function	identical protein binding
E	0043130	molecular_function	ubiquitin binding
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0043231	cellular_component	intracellular membrane-bounded organelle
E	0043328	biological_process	protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
E	0043332	cellular_component	mating projection tip
E	0046034	biological_process	ATP metabolic process
E	0050896	biological_process	response to stimulus
E	0051228	biological_process	mitotic spindle disassembly
E	0070651	biological_process	nonfunctional rRNA decay
E	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
E	0071630	biological_process	nuclear protein quality control by the ubiquitin-proteasome system
E	0072344	biological_process	rescue of stalled ribosome
E	0072671	biological_process	mitochondria-associated ubiquitin-dependent protein catabolic process
E	0097352	biological_process	autophagosome maturation
E	0120174	biological_process	stress-induced homeostatically regulated protein degradation pathway
E	1900182	biological_process	positive regulation of protein localization to nucleus
E	1990112	cellular_component	RQC complex
E	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process
E	1990171	biological_process	SCF complex disassembly in response to cadmium stress
G	0000837	cellular_component	Doa10p ubiquitin ligase complex
G	0000839	cellular_component	Hrd1p ubiquitin ligase ERAD-L complex
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005783	cellular_component	endoplasmic reticulum
G	0005789	cellular_component	endoplasmic reticulum membrane
G	0006274	biological_process	DNA replication termination
G	0006511	biological_process	ubiquitin-dependent protein catabolic process
G	0006515	biological_process	protein quality control for misfolded or incompletely synthesized proteins
G	0008270	molecular_function	zinc ion binding
G	0015031	biological_process	protein transport
G	0016020	cellular_component	membrane
G	0030894	cellular_component	replisome
G	0030970	biological_process	retrograde protein transport, ER to cytosol
G	0031625	molecular_function	ubiquitin protein ligase binding
G	0031965	cellular_component	nuclear membrane
G	0034098	cellular_component	VCP-NPL4-UFD1 AAA ATPase complex
G	0036266	cellular_component	Cdc48p-Npl4p-Vms1p AAA ATPase complex
G	0036503	biological_process	ERAD pathway
G	0042175	cellular_component	nuclear outer membrane-endoplasmic reticulum membrane network
G	0043130	molecular_function	ubiquitin binding
G	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
G	0048471	cellular_component	perinuclear region of cytoplasm
G	0051028	biological_process	mRNA transport
G	0051228	biological_process	mitotic spindle disassembly
G	0070651	biological_process	nonfunctional rRNA decay
G	0071629	biological_process	cytoplasm protein quality control by the ubiquitin-proteasome system
G	0072344	biological_process	rescue of stalled ribosome
G	0072665	biological_process	protein localization to vacuole
G	0072671	biological_process	mitochondria-associated ubiquitin-dependent protein catabolic process
G	1900182	biological_process	positive regulation of protein localization to nucleus
G	1990112	cellular_component	RQC complex
G	1990116	biological_process	ribosome-associated ubiquitin-dependent protein catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	binding site for residue ADP B 901

Chain	Residue
B	VAL489
B	GLY694
B	BEF903
C	ARG645
C	ARG648
B	PRO530
B	GLY531
B	GLY533
B	LYS534
B	THR535
B	LEU536
B	ILE666
B	GLN670

site_id	AC2
Number of Residues	4
Details	binding site for residue BEF B 902

Chain	Residue
B	THR262
B	ASP314
B	GLU315
B	ADP904

site_id	AC3
Number of Residues	5
Details	binding site for residue BEF B 903

Chain	Residue
B	THR535
B	ASP587
B	GLU588
B	ADP901
C	ARG648

site_id	AC4
Number of Residues	15
Details	binding site for residue ADP B 904

Chain	Residue
B	ILE216
B	GLY217
B	PRO257
B	GLY258
B	THR259
B	LYS261
B	THR262
B	LEU263
B	VAL390
B	GLY418
B	ALA419
B	ALA422
B	BEF902
C	ARG369
C	PHE370

site_id	AC5
Number of Residues	6
Details	binding site for residue BEF C 901

Chain	Residue
C	LYS261
C	THR262
C	GLU315
C	ADP903
D	ASP343
D	ARG372

site_id	AC6
Number of Residues	5
Details	binding site for residue BEF C 902

Chain	Residue
C	THR535
C	ASP587
C	GLU588
C	ADP904
D	ARG648

site_id	AC7
Number of Residues	13
Details	binding site for residue ADP C 903

Chain	Residue
C	ILE216
C	GLY217
C	THR259
C	GLY260
C	LYS261
C	THR262
C	LEU263
C	HIS394
C	GLY418
C	BEF901
D	ASP343
D	ARG369
D	PHE370

site_id	AC8
Number of Residues	14
Details	binding site for residue ADP C 904

Chain	Residue
C	PRO530
C	GLY531
C	THR532
C	GLY533
C	LYS534
C	THR535
C	LEU536
C	ILE666
C	GLY694
C	ALA695
C	LEU698
C	BEF902
D	ASP619
D	ARG645

site_id	AC9
Number of Residues	4
Details	binding site for residue BEF D 901

Chain	Residue
D	LYS261
D	THR262
E	ARG369
E	ADP902

site_id	AD1
Number of Residues	6
Details	binding site for residue BEF D 902

Chain	Residue
D	THR535
D	ASP587
D	ALA632
E	ASP619
E	ARG648
E	ADP901

site_id	AD2
Number of Residues	13
Details	binding site for residue ADP E 901

Chain	Residue
D	PRO530
D	GLY531
D	THR532
D	GLY533
D	LYS534
D	THR535
D	LEU536
D	ILE666
D	GLN670
D	GLY694
D	BEF902
E	ARG645
E	ARG648

site_id	AD3
Number of Residues	12
Details	binding site for residue ADP E 902

Chain	Residue
D	GLY258
D	THR259
D	GLY260
D	LYS261
D	THR262
D	LEU263
D	VAL390
D	GLY418
D	BEF901
E	ARG369
E	PHE370
D	ILE216

site_id	AD4
Number of Residues	8
Details	binding site for residue ADP E 903

Chain	Residue
E	GLY531
E	THR532
E	GLY533
E	LYS534
E	THR535
E	LEU536
E	PRO658
E	GLN670

site_id	AD5
Number of Residues	10
Details	binding site for residue ADP E 904

Chain	Residue
E	ASP215
E	ILE216
E	GLY258
E	THR259
E	GLY260
E	LEU263
E	MET264
E	VAL390
E	ALA419
E	ALA422

Functional Information from PROSITE/UniProt

site_id	PS00430
Number of Residues	72
Details	TONB_DEPENDENT_REC_1 TonB-dependent receptor (TBDR) proteins signature 1. mgeehkplldasgvdpreedktatailrrkkkdnmllvddainddnsviainsntmdklelfrg...................................................DTVLVKGK

Chain	Residue	Details
B	MET1-LYS72

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

Chain	Residue	Details
B	VAL351-ARG369
B	VAL627-ARG645

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

Chain	Residue	Details
H	LYS27-ASP52

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
H	GLY76
E	PRO257
E	ASN358
E	HIS394
B	ASN358
B	HIS394
C	PRO257
C	ASN358
C	HIS394
D	PRO257
D	ASN358
D	HIS394

site_id	SWS_FT_FI2
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:Q01853

Chain	Residue	Details
B	GLY531
C	GLY531
D	GLY531
E	GLY531

site_id	SWS_FT_FI3
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:18407956

Chain	Residue	Details
B	SER472
C	SER472
D	SER472
E	SER472

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17330950, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
B	SER519
C	SER519
D	SER519
E	SER519

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:18407956, ECO:0007744\|PubMed:19779198

Chain	Residue	Details
B	THR735
C	THR735
D	THR735
E	THR735

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17287358, ECO:0007744\|PubMed:17330950

Chain	Residue	Details
B	SER770
C	SER770
D	SER770
E	SER770

site_id	SWS_FT_FI7
Number of Residues	20
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744\|PubMed:22106047

Chain	Residue	Details
B	LYS305
C	LYS539
D	LYS305
D	LYS322
D	LYS346
D	LYS522
D	LYS539
E	LYS305
E	LYS322
E	LYS346
E	LYS522
B	LYS322
E	LYS539
B	LYS346
B	LYS522
B	LYS539
C	LYS305
C	LYS322
C	LYS346
C	LYS522

site_id	SWS_FT_FI8
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:12872131

Chain	Residue	Details
E	LYS594
E	LYS673
B	LYS594
B	LYS673
C	LYS594
C	LYS673
D	LYS594
D	LYS673

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)