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Cryo-EM structure of the J-K-St region of EMCV IRES in complex with eIF4G-HEAT1 and eIF4A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8041750	3002019	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
B	PF02854	MIF4G domain (MIF4G)	MIF4G domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Eukaryotic initiation factor 4A-I	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity RNA binding double-stranded RNA binding RNA cap binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity RNA binding double-stranded RNA binding RNA cap 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 mRNA 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, acting on RNA RNA helicase activity ATP-dependent activity, acting on RNA	cellular biosynthetic process cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular process protein metabolic process macromolecule metabolic process cytoplasmic translation cytoplasmic translational initiation cellular biosynthetic process cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular process protein metabolic process macromolecule metabolic process cytoplasmic translation cytoplasmic translational initiation regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process	membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane nuclear stress granule nucleus intracellular membrane-bounded organelle ribonucleoprotein granule intracellular organelle intracellular non-membrane-bounded organelle supramolecular complex non-membrane-bounded organelle perinuclear region of cytoplasm protein-containing complex eukaryotic translation initiation factor 4F complex RNA cap binding complex intracellular protein-containing complex
B	Eukaryotic translation initiation factor 4 gamma 1	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding eukaryotic initiation factor 4E binding protein binding translation initiation factor binding RNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding nucleic acid binding translation initiation factor activity translation factor activity, RNA binding eukaryotic initiation factor 4E binding protein binding translation initiation factor binding RNA 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 mRNA binding molecular adaptor activity	regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process cellular biosynthetic process cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process translational initiation metabolic process protein metabolic process macromolecule metabolic process positive regulation of protein metabolic process regulation of protein metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of metabolic process positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis eukaryotic translation initiation factor 4F complex assembly regulation of cellular component biogenesis regulation of eukaryotic translation initiation factor 4F complex assembly cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly positive regulation of eukaryotic translation initiation factor 4F complex assembly protein-containing complex assembly cellular response to stimulus response to stimulus positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process post-transcriptional regulation of gene expression regulation of translation in response to stress cellular response to stress positive regulation of biosynthetic process response to stress positive regulation of translation in response to stress response to endoplasmic reticulum stress positive regulation of translation in response to endoplasmic reticulum stress regulation of biosynthetic process regulation of translation in response to endoplasmic reticulum stress regulation of cellular metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process positive regulation of cellular biosynthetic process regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process regulation of peptidyl-threonine phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process peptidyl-amino acid modification peptidyl-threonine modification protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation negative regulation of metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of peptidyl-threonine phosphorylation negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation peptidyl-threonine phosphorylation cap-dependent translational initiation cytoplasmic translation cytoplasmic translational initiation cellular response to nutrient levels response to nutrient levels multicellular organismal process regulation of presynapse assembly multicellular organism development regulation of presynapse organization cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization regulation of biological quality regulation of synapse assembly system development developmental process presynapse organization nervous system development regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly presynapse assembly tube development animal organ development respiratory tube development lung development respiratory system development multicellular organismal-level homeostasis homeostatic process energy homeostasis positive regulation of RNA binding positive regulation of mRNA cap binding regulation of binding regulation of mRNA binding positive regulation of binding regulation of RNA binding positive regulation of mRNA binding regulation of molecular function positive regulation of molecular function regulation of mRNA cap binding positive regulation of phosphorylation regulation of peptidyl-serine phosphorylation positive regulation of phosphate metabolic process peptidyl-serine modification positive regulation of protein modification process peptidyl-serine phosphorylation positive regulation of protein phosphorylation positive regulation of phosphorus metabolic process positive regulation of peptidyl-serine phosphorylation negative regulation of translation miRNA-mediated gene silencing by inhibition of translation regulatory ncRNA-mediated post-transcriptional gene silencing negative regulation of cellular biosynthetic process regulatory ncRNA-mediated gene silencing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing positive regulation of protein localization to cell periphery protein localization regulation of localization cellular localization protein localization to cell periphery regulation of protein localization regulation of protein localization to cell periphery localization regulation of cellular localization cellular macromolecule localization macromolecule localization positive regulation of protein localization regulation of cellular response to stress regulation of response to stimulus regulation of response to stress cellular developmental process generation of neurons neurogenesis neuron differentiation cell differentiation regulation of cell cycle phase transition cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle cell cycle regulation of cell cycle cell cycle process positive regulation of G1/S transition of mitotic cell cycle regulation of cell cycle process positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle G1/S phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle positive regulation of cell cycle phase transition G1/S transition of mitotic cell cycle mitotic cell cycle phase transition response to alcohol response to chemical response to oxygen-containing compound response to ethanol regulation of developmental process regulation of cell differentiation positive regulation of neuron differentiation positive regulation of developmental process positive regulation of cell differentiation regulation of neuron differentiation regulation of translational initiation negative regulation of cellular catabolic process negative regulation of catabolic process catabolic process autophagy regulation of catabolic process regulation of autophagy cellular catabolic process negative regulation of autophagy regulation of cellular catabolic process process utilizing autophagic mechanism behavioral defense response behavior fear response behavioral fear response defense response multicellular organismal response to stress	intracellular anatomical structure cytoplasmic ribonucleoprotein granule cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule membrane cytosol ribosome intracellular anatomical structure cytoplasmic ribonucleoprotein granule cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule membrane cytosol ribosome protein-containing complex eukaryotic translation initiation factor 4F complex RNA cap binding complex intracellular protein-containing complex postsynapse synapse cell junction membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	IRES RNA (J-K-St)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A	IPR044728	ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain	Domain
A	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
A	IPR011545	DEAD/DEAH box helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B	IPR016024	Armadillo-type fold	Homologous Superfamily
B	IPR003307	W2 domain	Domain
B	IPR003891	Initiation factor eIF-4 gamma, MA3	Domain
B	IPR045208	IF4G	Unknown
B	IPR003890	MIF4G-like, type 3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P60842	HIV infectious disease atrial fibrillation esophageal squamous cell carcinoma metabolic syndrome X triple-negative breast carcinoma brain glioma glioblastoma IgA glomerulonephritis neuroblastoma uterine corpus leiomyoma cutaneous melanoma HIV Coinfection melanoma skin basal cell carcinoma
B	Pharos: Q04637	Parkinson disease 18, autosomal dominant, susceptibility to Parkinson disease adenoma Autosomal dominant late onset Parkinson disease glioblastoma neurodegenerative disease amyotrophic lateral sclerosis colorectal cancer intellectual disability non-small cell lung carcinoma astrocytic tumor gastric carcinoma large cell medulloblastoma ovarian cancer

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.