5X4L | pdb_00005x4l

Crystal structure of the UBX domain of human UBXD7 in complex with p97 N domain

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5x4ld_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5x4lc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5x4lb1	All beta proteins	Double psi beta-barrel	ADC-like	Cdc48 N-terminal domain-like	Membrane fusion ATPase p97 N-terminal domain , P97-Nn	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5x4lb2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	Cdc48 domain 2-like	Membrane fusion atpase p97 domain 2, P97-Nc	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5x4la1	All beta proteins	Double psi beta-barrel	ADC-like	Cdc48 N-terminal domain-like	Membrane fusion ATPase p97 N-terminal domain , P97-Nn	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5x4la2	Alpha and beta proteins (a+b)	Cdc48 domain 2-like	Cdc48 domain 2-like	Cdc48 domain 2-like	Membrane fusion atpase p97 domain 2, P97-Nc	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5x4la3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e5x4lD1	A: Thioredoxin-like	X: Nucleic acid-binding protein	H: Chelatase-like	T: AHAS-like_ACT	F:	ECOD (20:10:01)
C		e5x4lC1	A: Thioredoxin-like	X: Nucleic acid-binding protein	H: Chelatase-like	T: AHAS-like_ACT	F:	ECOD (20:10:01)
B		e5x4lB1	A: Thioredoxin-like	X: Nucleic acid-binding protein	H: Chelatase-like	T: AHAS-like_ACT	F:	ECOD (20:10:01)
A		e5x4lA1	A: Thioredoxin-like	X: Nucleic acid-binding protein	H: Chelatase-like	T: AHAS-like_ACT	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
B	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
A, B	PF02933	Cell division protein 48 (CDC48), domain 2 (CDC48_2)	Cell division protein 48 (CDC48), domain 2	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 C-terminus. The VAT-N domain found in AAA ATPases Pfam:PF00004 is a substrate 185-residue recognition domain [1].	Domain
A, B	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
C, D	UBX domain-containing protein 7	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding ubiquitin binding ubiquitin-like protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex VCP-NPL4-UFD1 AAA ATPase complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane cytosol nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B	Transitional endoplasmic reticulum ATPase	protein phosphatase binding phosphatase binding protein binding binding enzyme 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 protein phosphatase binding phosphatase binding protein binding binding enzyme 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 ubiquitin-modified protein reader activity protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein domain specific binding lipid binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity deubiquitinase activator activity peptidase activator 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 MHC class I protein binding signaling receptor binding MHC protein binding polyubiquitin modification-dependent protein binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding ubiquitin-specific protease binding protease binding ADP binding identical protein binding protein-containing complex binding BAT3 complex binding RNA binding nucleic acid binding	catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein deubiquitination catabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus protein deubiquitination regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein modification by small protein removal positive regulation of macromolecule metabolic process protein metabolic process protein modification process regulation of protein modification by small protein conjugation or removal regulation of protein K63-linked deubiquitination positive regulation of cellular process positive regulation of protein K63-linked deubiquitination positive regulation of protein modification by small protein conjugation or removal regulation of biological process regulation of post-translational protein modification protein K63-linked deubiquitination regulation of protein metabolic process positive regulation of protein deubiquitination biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of protein deubiquitination macromolecule modification macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation or removal DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA damage response interstrand cross-link repair DNA repair translesion synthesis nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process DNA replication biosynthetic process DNA biosynthetic process positive regulation of proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process localization cellular localization transport establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport cytoplasm protein quality control protein quality control for misfolded or incompletely synthesized proteins cellular component biogenesis cellular component organization cellular component assembly aggresome assembly inclusion body assembly cellular component organization or biogenesis cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein response to topologically incorrect protein signaling endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication signal transduction response to endoplasmic reticulum stress establishment of protein localization regulation of localization protein localization to chromatin regulation of protein localization protein localization to chromosome macromolecule localization protein localization to organelle regulation of protein localization to chromatin intracellular protein localization nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process NAD+ metabolic process regulation of cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality regulation of mitochondrial membrane potential positive regulation of mitochondrial membrane potential positive regulation of membrane potential regulation of membrane potential protein exit from endoplasmic reticulum ERAD pathway endoplasmic reticulum to cytosol transport protein transport response to chemical retrograde protein transport, ER to cytosol intracellular protein transport macroautophagy positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway protein-DNA covalent cross-linking repair cellular component disassembly protein-containing complex organization protein-containing complex disassembly autophagosome maturation spindle disassembly microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization organelle 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 positive regulation of cellular component organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death protein ubiquitination protein modification by small protein conjugation cellular response to arsenic-containing substance response to oxygen-containing compound response to arsenic-containing substance cellular response to oxygen-containing compound cellular response to chemical stimulus response to arsenite ion cellular response to arsenite ion hippo signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of cell communication negative regulation of cellular process negative regulation of response to stimulus negative regulation of hippo signaling negative regulation of signal transduction regulation of hippo signaling nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process positive regulation of phosphate metabolic process purine ribonucleoside triphosphate biosynthetic process positive regulation of nucleotide biosynthetic process regulation of nucleotide biosynthetic process regulation of ATP metabolic process ribonucleotide biosynthetic process purine nucleoside triphosphate biosynthetic process regulation of small molecule metabolic process positive regulation of purine nucleotide biosynthetic process regulation of nucleotide metabolic process regulation of nucleobase-containing compound metabolic process ribose phosphate biosynthetic process positive regulation of phosphorus metabolic process regulation of purine nucleotide metabolic process ribonucleoside triphosphate biosynthetic process positive regulation of ATP metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process positive regulation of nucleotide metabolic process ribonucleotide metabolic process positive regulation of biosynthetic process purine ribonucleoside triphosphate metabolic process purine-containing compound biosynthetic process purine nucleoside triphosphate metabolic process regulation of biosynthetic process carbohydrate derivative biosynthetic process regulation of purine nucleotide biosynthetic process nucleoside triphosphate biosynthetic process positive regulation of purine nucleotide metabolic process positive regulation of ATP biosynthetic process regulation of ATP biosynthetic process positive regulation of small molecule metabolic process cellular respiration aerobic respiration energy derivation by oxidation of organic compounds regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration oxidative phosphorylation positive regulation of oxidative phosphorylation positive regulation of cellular respiration regulation of oxidative phosphorylation protein-RNA complex disassembly protein-RNA complex organization stress granule disassembly flavin-containing compound metabolic process flavin adenine dinucleotide catabolic process organophosphate catabolic process flavin adenine dinucleotide metabolic process nucleoside phosphate catabolic process nucleobase-containing compound catabolic process flavin-containing compound catabolic process nucleotide catabolic process viral genome replication viral process viral life cycle negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway smoothened signaling pathway negative regulation of protein localization to chromatin negative regulation of protein localization endoplasmic reticulum stress-induced pre-emptive quality control double-strand break repair endosome to lysosome transport lysosomal transport endosomal transport endosome to lysosome transport via multivesicular body sorting pathway multivesicular body sorting pathway vacuolar transport endosome transport via multivesicular body sorting pathway	ciliary transition zone membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol cytoplasmic ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex ciliary transition zone membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cytosol cytoplasmic ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex intracellular membraneless organelle intracellular organelle ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment Derlin-1 retrotranslocation complex nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane peptidase complex proteasome complex endopeptidase complex extracellular region vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen secretory granule lumen intracellular organelle lumen cytoplasmic vesicle organelle lumen secretory granule secretory vesicle vesicle site of double-strand break site of DNA damage chromosome extracellular exosome extracellular vesicle extracellular organelle extracellular space extracellular membrane-bounded organelle ciliary tip synapse cell junction glutamatergic synapse perinuclear region of cytoplasm VCP-NPL4-UFD1 AAA ATPase complex cytoplasmic ribonucleoprotein granule ribonucleoprotein granule supramolecular complex cytoplasmic stress granule lytic vacuole vacuolar lumen lysosome azurophil granule vacuole azurophil granule lumen primary lysosome ficolin-1-rich granule ficolin-1-rich granule lumen nucleus nucleoplasm nuclear lumen ATPase complex VCP-NSFL1C complex lipid droplet

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR054109	UBA-like domain	Domain
C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
C, D	IPR050730	UBX domain-containing protein	Family
C, D	IPR009060	UBA-like superfamily	Homologous Superfamily
C, D	IPR006577	UAS	Domain
C, D	IPR017346	UBX domain-containing protein 2/7	Family
C, D	IPR001012	UBX domain	Domain
C, D	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B	IPR003959	ATPase, AAA-type, core	Domain
A, B	IPR005938	AAA ATPase, CDC48 family	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR029067	CDC48 domain 2-like superfamily	Homologous Superfamily
A, B	IPR003338	CDC48, N-terminal subdomain	Domain
A, B	IPR004201	CDC48, domain 2	Domain
A, B	IPR009010	Aspartate decarboxylase-like domain superfamily	Homologous Superfamily
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR041569	AAA ATPase, AAA+ lid domain	Domain
A, B	IPR050168	AAA ATPase domain-containing protein	Family
A, B	IPR003960	ATPase, AAA-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: O94888	astrocytic tumor large cell medulloblastoma non-small cell lung carcinoma ovarian cancer pituitary cancer sarcoidosis atypical teratoid rhabdoid tumor malignant mesothelioma oligodendroglioma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor tuberculosis glioblastoma medulloblastoma osteosarcoma astrocytic tumor large cell medulloblastoma non-small cell lung carcinoma ovarian cancer pituitary cancer sarcoidosis atypical teratoid rhabdoid tumor malignant mesothelioma oligodendroglioma pancreatic ductal adenocarcinoma primitive neuroectodermal tumor tuberculosis glioblastoma medulloblastoma osteosarcoma Pick disease psoriasis
A, B	Pharos: P55072	amyotrophic lateral sclerosis Charcot-Marie-Tooth disease type 2Y inclusion body myopathy with Paget disease of bone and frontotemporal dementia frontotemporal dementia and/or amyotrophic lateral sclerosis 6 Charcot-Marie-Tooth disease Stevens-Johnson syndrome inclusion body myopathy with Paget disease of bone and frontotemporal dementia type 1 behavioral variant of frontotemporal dementia peripheral neuropathy neurodegenerative disease Mycoplasma-Induced Stevens-Johnson Syndrome osteosarcoma peripheral nervous system disease plasma cell myeloma prostate cancer amyotrophic lateral sclerosis Charcot-Marie-Tooth disease type 2Y inclusion body myopathy with Paget disease of bone and frontotemporal dementia frontotemporal dementia and/or amyotrophic lateral sclerosis 6 Charcot-Marie-Tooth disease Stevens-Johnson syndrome inclusion body myopathy with Paget disease of bone and frontotemporal dementia type 1 behavioral variant of frontotemporal dementia peripheral neuropathy neurodegenerative disease Mycoplasma-Induced Stevens-Johnson Syndrome osteosarcoma peripheral nervous system disease plasma cell myeloma prostate cancer dementia lymphoplasmacytic lymphoma myopathy ovarian cancer psoriasis arthrogryposis bone Paget disease motor peripheral neuropathy pancreatic ductal adenocarcinoma Pick disease progressive non-fluent aphasia spastic paraplegia-Paget disease of bone syndrome astrocytic tumor toxic epidermal necrolysis cytomegalovirus infection distal myopathy frontotemporal dementia with motor neuron disease limb-girdle muscular dystrophy

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.