3AGZ | pdb_00003agz

Crystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Histone	e3agzB3	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: Histone	ECOD (v294.1)
B	DZF_C	e3agzB2	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DZF_C	ECOD (v294.1)
A	TetR_N	e3agzA1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: L30e-like	T: L30e-like	F: TetR_N	ECOD (v294.1)
A	DZF_C	e3agzA2	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DZF_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.260.20	Mainly Beta	Sandwich	HSP40/DNAj peptide-binding domain	Urease metallochaperone UreE, N-terminal domain	CATH (4.3.0)
A	2.60.260.20	Mainly Beta	Sandwich	HSP40/DNAj peptide-binding domain	Urease metallochaperone UreE, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01556	DnaJ C terminal domain (DnaJ_C)	DnaJ C terminal domain	This family consists of the C terminal region of the DnaJ protein. It is always found associated with Pfam:PF00226 and Pfam:PF00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after ...	This family consists of the C terminal region of the DnaJ protein. It is always found associated with Pfam:PF00226 and Pfam:PF00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and CTDII, both incorporated in this family are necessary for maintaining the J-domains in their specific relative positions [2]. Structural analysis of PDB:1nlt shows that PF00684 is nested within this DnaJ C-terminal region [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, E, F	peptide of Heat shock cognate 71 kDa protein	protein binding binding C3HC4-type RING finger domain binding protein domain specific binding protein-containing complex destabilizing activity ATP-dependent protein disaggregase activity ATP-dependent activity protein-containing complex binding MHC protein complex binding MHC class II protein complex binding heat shock protein binding protein-folding chaperone binding protein-macromolecule adaptor activity molecular adaptor activity protein binding binding C3HC4-type RING finger domain binding protein domain specific binding protein-containing complex destabilizing activity ATP-dependent protein disaggregase activity ATP-dependent activity protein-containing complex binding MHC protein complex binding MHC class II protein complex binding heat shock protein binding protein-folding chaperone binding protein-macromolecule adaptor activity molecular adaptor activity 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 cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity RNA binding nucleic acid binding ATP-dependent protein folding chaperone protein folding chaperone unfolded protein binding 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 signaling receptor binding G protein-coupled receptor binding	protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of biological process positive regulation of programmed cell death regulation of cellular process protein refolding primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of ferroptosis regulation of ferroptosis ferroptosis programmed cell death positive regulation of cellular process cellular response to stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to stimulus regulation of NLRP3 inflammasome complex assembly negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction negative regulation of NLRP3 inflammasome complex assembly positive regulation of immune system process innate immune response-activating signaling pathway negative regulation of cellular component organization immune response response to other organism regulation of innate immune response response to external stimulus regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular component organization regulation of response to external stimulus intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus cellular component organization regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response negative regulation of cellular process protein-containing complex assembly response to external biotic stimulus cellular component organization or biogenesis regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus protein-containing complex organization defense response to symbiont regulation of cellular component biogenesis negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication negative regulation of inflammasome-mediated signaling pathway response to topologically incorrect protein response to unfolded protein regulation of protein complex stability regulation of biological quality response to lipid response to endogenous stimulus cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to steroid hormone cellular response to lipid cellular response to steroid hormone stimulus cellular response to hormone stimulus cellular component disassembly clathrin coat disassembly transport protein-containing complex disassembly establishment of localization vesicle-mediated transport vesicle uncoating localization protein depolymerization regulation of supramolecular fiber organization negative regulation of supramolecular fiber organization supramolecular fiber organization cellular response to nutrient levels response to nutrient levels cellular response to stress response to starvation cellular response to starvation regulation of protein stability establishment of protein localization cellular localization catabolic process protein targeting to vacuole involved in autophagy protein targeting autophagy establishment of protein localization to vacuole protein targeting to lysosome involved in chaperone-mediated autophagy lysosomal transport macromolecule catabolic process chaperone-mediated autophagy protein targeting to lysosome establishment of localization in cell intracellular protein localization process utilizing autophagic mechanism protein targeting to vacuole intracellular transport protein localization to vacuole protein catabolic process protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle macromolecule localization vacuolar transport intracellular protein transport RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription negative regulation of metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process nucleoside phosphate metabolic process ribose phosphate metabolic process purine nucleoside triphosphate metabolic process ATP metabolic process carbohydrate derivative metabolic process nucleotide metabolic process purine-containing compound metabolic process purine nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process phosphorus metabolic process regulation of localization protein import regulation of protein localization regulation of transport regulation of establishment of protein localization regulation of protein transport regulation of protein import RNA splicing mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion membrane organization chaperone-mediated autophagy translocation complex disassembly	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol clathrin-sculpted gamma-aminobutyric acid transport vesicle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol clathrin-sculpted gamma-aminobutyric acid transport vesicle clathrin-sculpted vesicle intracellular vesicle clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane intracellular membrane-bounded organelle intracellular organelle coated vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle coated vesicle organelle membrane clathrin-coated vesicle membrane protein-containing complex protein folding chaperone complex intracellular protein-containing complex vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome anchoring junction cell junction focal adhesion cell-substrate junction nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen pigment granule melanosome vacuolar lumen lysosomal lumen Prp19 complex cell periphery plasma membrane ficolin-1-rich granule endomembrane system ficolin-1-rich granule lumen secretory granule secretory vesicle nucleoplasm blood microparticle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex side of membrane lumenal side of membrane lumenal side of lysosomal membrane
A, B	DnaJ homolog subfamily B member 1	molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity ATPase activator activity molecular function activator activity protein binding binding Hsp70 protein binding protein-folding chaperone binding heat shock protein binding transcription corepressor activity transcription regulator activity transcription coregulator activity unfolded protein binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity ATPase activator activity molecular function activator activity protein binding binding Hsp70 protein binding protein-folding chaperone binding heat shock protein binding transcription corepressor activity transcription regulator activity transcription coregulator activity unfolded protein binding cell adhesion molecule binding cadherin binding protein folding chaperone ATPase binding enzyme binding	regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization regulation of inclusion body assembly biological regulation negative regulation of biological process inclusion body assembly regulation of cellular component biogenesis cellular component biogenesis cellular component organization cellular component assembly negative regulation of cellular process cellular process regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization regulation of inclusion body assembly biological regulation negative regulation of biological process inclusion body assembly regulation of cellular component biogenesis cellular component biogenesis cellular component organization cellular component assembly negative regulation of cellular process cellular process cellular component organization or biogenesis negative regulation of inclusion body assembly protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation response to stimulus response to topologically incorrect protein response to stress response to unfolded protein cellular response to stimulus cellular response to heat cellular response to stress response to heat response to abiotic stimulus response to temperature stimulus positive regulation of biological process positive regulation of protein folding regulation of protein folding positive regulation of cellular process developmental process multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development system development RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular response to heat regulation of cellular response to stress regulation of response to stimulus regulation of response to stress	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle cytoplasm cytosol nucleoplasm synapse cell junction glutamatergic synapse neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse cell body neuronal cell body sperm head

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, E, F	IPR013126	Heat shock protein 70 family	Family
C, D, E, F	IPR018181	Heat shock protein 70, conserved site	Conserved Site
C, D, E, F	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
C, D, E, F	IPR029048	Heat shock protein 70kD, C-terminal domain superfamily	Homologous Superfamily
C, D, E, F	IPR029047	Heat shock protein 70kD, peptide-binding domain superfamily	Homologous Superfamily
A, B	IPR001623	DnaJ domain	Domain
A, B	IPR051339	DnaJ homolog subfamily B	Family
A, B	IPR018253	DnaJ domain, conserved site	Conserved Site
A, B	IPR002939	Chaperone DnaJ, C-terminal	Domain
A, B	IPR036869	Chaperone J-domain superfamily	Homologous Superfamily
A, B	IPR008971	HSP40/DnaJ peptide-binding	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D, E, F	Pharos: P11142	spinocerebellar ataxia type 17 squamous cell carcinoma acute coronary syndrome tubular adenocarcinoma adenocarcinoma granular cell carcinoma Adenocarcinoma, Oxyphilic gastric cancer hereditary diffuse gastric adenocarcinoma cribriform carcinoma gastric neoplasm ischemia reperfusion injury cribriform carcinoma of breast oral cavity neoplasm
A, B	Pharos: P25685	astrocytic tumor exocrine pancreatic carcinoma lymphoplasmacytic lymphoma nephrolithiasis plasma cell myeloma spina bifida bipolar disorder fibrolamellar hepatocellular carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma psoriasis tuberculosis esophageal adenocarcinoma glioblastoma medulloblastoma astrocytic tumor exocrine pancreatic carcinoma lymphoplasmacytic lymphoma nephrolithiasis plasma cell myeloma spina bifida bipolar disorder fibrolamellar hepatocellular carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma psoriasis tuberculosis esophageal adenocarcinoma glioblastoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia sinusitis

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.