1NTG

Crystal Structure of the EMAP II-like Cytokine Released from human tyrosyl-tRNA Synthetase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d1ntga1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Myf domain	C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1ntga2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1ntgb1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Myf domain	C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1ntgb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1ntgc1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Myf domain	C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1ntgc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1ntgd1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Myf domain	C-terminal domain of metazoan tyrosyl-tRNA synthetase, TyrRS	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1ntgd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Myf domain	8021221	4001906	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8033601	3000135	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8033601	3000135	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleic acid-binding proteins	8033601	3000135	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleic acid-binding proteins	8033601	3000135	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	tRNA_bind	e1ntgA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_bind	ECOD (1.6)
B	tRNA_bind	e1ntgB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_bind	ECOD (1.6)
C	tRNA_bind	e1ntgC1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_bind	ECOD (1.6)
D	tRNA_bind	e1ntgD1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01588	Putative tRNA binding domain (tRNA_bind)	Putative tRNA binding domain	This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [2], human tyrosyl-tRNA synthetase [1], and endothelial-monocyte activating polypept ...	This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [2], human tyrosyl-tRNA synthetase [1], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases [2]. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme [2]. This domain may perform a common function in tRNA aminoacylation [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Tyrosyl-tRNA synthetase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity tyrosine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity RNA binding nucleic acid binding tRNA binding protein binding interleukin-8 receptor binding signaling receptor binding cytokine receptor binding CXCR chemokine receptor binding G protein-coupled receptor binding chemokine receptor binding	cellular process apoptotic process cell death programmed cell death response to nutrient levels response to stimulus response to stress response to starvation amino acid activation tyrosyl-tRNA aminoacylation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process cellular process apoptotic process cell death programmed cell death response to nutrient levels response to stimulus response to stress response to starvation amino acid activation tyrosyl-tRNA aminoacylation tRNA aminoacylation RNA metabolic process primary metabolic process amino acid metabolic process translation gene expression tRNA aminoacylation for protein translation macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process biosynthetic process metabolic process macromolecule metabolic process protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm cellular anatomical structure intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002547	tRNA-binding domain	Domain
A, B, C, D	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B, C, D	IPR051270	Tyrosine-tRNA ligase and regulatory protein	Family
A, B, C, D	IPR002307	Tyrosine-tRNA ligase	Family
A, B, C, D	IPR002305	Aminoacyl-tRNA synthetase, class Ic	Family
A, B, C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P54577	Charcot-Marie-Tooth disease dominant intermediate C peripheral neuropathy Charcot-Marie-Tooth disease astrocytic tumor dermatomyositis malignant pancreatic neoplasm ovarian cancer diabetes mellitus motor peripheral neuropathy pancreatic ductal adenocarcinoma malignant colon neoplasm neurodegenerative disease peripheral nervous system disease

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.