4RV0 | pdb_00004rv0

Crystal structure of TN complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G	d4rv0g1	All beta proteins	Double psi beta-barrel	ADC-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
G	d4rv0g2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
G	d4rv0g3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
E	d4rv0e1	All beta proteins	Double psi beta-barrel	ADC-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
E	d4rv0e2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
E	d4rv0e3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C	d4rv0c1	All beta proteins	Double psi beta-barrel	ADC-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C	d4rv0c2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C	d4rv0c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d4rv0a1	All beta proteins	Double psi beta-barrel	ADC-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d4rv0a2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	automated matches	automated matches	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A	d4rv0a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	UN_NPL4	e4rv0H1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UN_NPL4	ECOD (1.6)
F	UN_NPL4	e4rv0F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UN_NPL4	ECOD (1.6)
D	UN_NPL4	e4rv0D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UN_NPL4	ECOD (1.6)
B	UN_NPL4	e4rv0B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UN_NPL4	ECOD (1.6)
G	CDC48_N	e4rv0G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
G	CDC48_2	e4rv0G2	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
E	CDC48_N	e4rv0E2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
E	CDC48_2	e4rv0E1	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
C	CDC48_N	e4rv0C2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
C	CDC48_2	e4rv0C1	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)
A	CDC48_N	e4rv0A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
A	CDC48_2	e4rv0A1	A: a+b two layers	X: Cdc48 domain 2-like (From Topology)	H: Cdc48 domain 2-like (From Topology)	T: Cdc48 domain 2-like	F: CDC48_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
G	3.10.330.10	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
E	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
E	3.10.330.10	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
C	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
C	3.10.330.10	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
A	3.10.330.10	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF11543	Nuclear pore localisation protein NPL4 (UN_NPL4)	Nuclear pore localisation protein NPL4	-	Family
A, C, E, G	PF02359	Cell division protein 48 (CDC48), N-terminal domain (CDC48_N)	Cell division protein 48 (CDC48), N-terminal domain	This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at t ...	This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate 185-residue recognition domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Nuclear protein localization protein 4 homolog	protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding polyubiquitin modification-dependent protein binding protein binding binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding polyubiquitin modification-dependent protein binding K11-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process signal transduction regulation of smoothened signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of cell communication proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process cellular response to virus biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
A, C, E, G	Transitional endoplasmic reticulum ATPase TER94	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding polyubiquitin modification-dependent protein binding protein binding modification-dependent protein binding molecular sequestering activity protein sequestering activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism cellular component disassembly protein-containing complex organization protein-containing complex disassembly autophagosome maturation spindle disassembly microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization mitotic cell cycle process organelle disassembly mitotic spindle disassembly microtubule-based process cell cycle cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process hippo signaling negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction negative regulation of hippo signaling regulation of hippo signaling biological process involved in interspecies interaction between organisms positive regulation of viral life cycle positive regulation of viral process viral life cycle modulation by symbiont of entry into host biological process involved in interaction with host biological process involved in symbiotic interaction regulation of viral entry into host cell regulation of viral life cycle regulation of viral process symbiont entry into host cell viral process symbiont entry into host positive regulation of viral entry into host cell positive regulation by symbiont of entry into host regulation of biological process involved in symbiotic interaction developmental process multicellular organismal process sexual reproduction cellular developmental process reproductive process cellularization multicellular organismal reproductive process cell development pole cell formation developmental process involved in reproduction gamete generation multicellular organism development anatomical structure morphogenesis pole cell development cell differentiation anatomical structure development anatomical structure formation involved in morphogenesis regulation of localization blastoderm segmentation anterior/posterior pattern specification anterior/posterior axis specification, embryo cellular process involved in reproduction in multicellular organism female gamete generation pole plasm oskar mRNA localization oocyte development cellular component biogenesis cellular component assembly cell maturation RNA localization pole plasm mRNA localization pole plasm RNA localization embryonic pattern specification regulation of intracellular mRNA localization oocyte anterior/posterior axis specification cytoplasm organization developmental maturation anatomical structure maturation maternal determination of anterior/posterior axis, embryo germ cell development intracellular mRNA localization involved in anterior/posterior axis specification axis specification segmentation pattern specification process embryo development tripartite regional subdivision embryonic axis specification regulation of pole plasm oskar mRNA localization anterior/posterior axis specification oocyte axis specification oocyte construction intracellular mRNA localization oogenesis regionalization pole plasm assembly intracellular mRNA localization involved in pattern specification process macromolecule localization oocyte differentiation cellular homeostasis homeostatic process muscle cell cellular homeostasis endoplasmic reticulum organization endoplasmic reticulum membrane organization endoplasmic reticulum membrane fusion endomembrane system organization cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development system development plasma membrane bounded cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons neuron development negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway smoothened signaling pathway protein exit from endoplasmic reticulum cellular localization establishment of protein localization nitrogen compound transport ERAD pathway cellular response to stress response to stress establishment of localization in cell intracellular protein localization response to endoplasmic reticulum stress endoplasmic reticulum to cytosol transport intracellular transport response to nitrogen compound protein transport response to chemical retrograde protein transport, ER to cytosol intracellular protein transport lysosome organization vacuole organization lytic vacuole organization lysosomal membrane organization Golgi organization cellular response to virus response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus larval midgut histolysis larval midgut cell programmed cell death instar larval or pupal development metamorphosis anatomical structure regression programmed cell death involved in cell development instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cytoplasm cytosol vacuolar membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane lysosome autolysosome secondary lysosome protein-containing complex organelle subcompartment membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule pole plasm membraneless organelle supramolecular complex cell periphery plasma membrane fusome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR007717	Nuclear pore localisation protein NPL4, C-terminal	Domain
B, D, F, H	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B, D, F, H	IPR007716	NPL4, zinc-binding putative	Domain
B, D, F, H	IPR016563	Nuclear protein localization protein 4	Family
B, D, F, H	IPR037518	MPN domain	Domain
B, D, F, H	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR001876	Zinc finger, RanBP2-type	Domain
B, D, F, H	IPR024682	Nuclear pore localisation protein Npl4, ubiquitin-like domain	Domain
A, C, E, G	IPR003959	ATPase, AAA-type, core	Domain
A, C, E, G	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E, G	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A, C, E, G	IPR005938	AAA ATPase, CDC48 family	Family
A, C, E, G	IPR003338	CDC48, N-terminal subdomain	Domain
A, C, E, G	IPR004201	CDC48, domain 2	Domain
A, C, E, G	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR003593	AAA+ ATPase domain	Domain
A, C, E, G	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, C, E, G	IPR015415	Spastin/Vps4, C-terminal	Domain
A, C, E, G	IPR050168	AAA ATPase domain-containing protein	Family
A, C, E, G	IPR003960	ATPase, AAA-type, conserved site	Conserved Site