2ZU6

crystal structure of the eIF4A-PDCD4 complex

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)
F	d2zu6f1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Initiation factor 4a	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2zu6a1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Initiation factor 4a	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2zu6a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2zu6c1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Initiation factor 4a	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2zu6d1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Initiation factor 4a	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2zu6d3	Artifacts	Tags	Tags	Tags	N-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	SCOP2B Superfamily	RecA-like P-loop NTPases	8041750	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8041750	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8041750	3002019	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	ARM repeat-like	8086320	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8086320	3000116	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)
F	DEAD	e2zu6F2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
F	Helicase_C_1	e2zu6F1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
A	DEAD	e2zu6A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
A	Helicase_C_1	e2zu6A2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
C	DEAD	e2zu6C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
C	Helicase_C_1	e2zu6C2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
D	DEAD	e2zu6D1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
D	Helicase_C_1	e2zu6D2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_1	ECOD (1.6)
E	MA3	e2zu6E4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MA3	ECOD (1.6)
B	MA3	e2zu6B4	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MA3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.25.40.180	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, D, F	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, C, D, F	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, E	PF02847	MA3 domain (MA3)	MA3 domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, D, F	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	biosynthetic process translational initiation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process cytoplasmic translation cytoplasmic translational initiation regulation of cellular process positive regulation of DNA-templated transcription biosynthetic process translational initiation metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic 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 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 macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic 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	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane 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 membraneless organelle intracellular membrane-bounded organelle ribonucleoprotein granule intracellular organelle membraneless organelle supramolecular complex perinuclear region of cytoplasm protein-containing complex eukaryotic translation initiation factor 4F complex RNA cap binding complex intracellular protein-containing complex
B, E	Programmed cell death protein 4	RNA binding binding organic cyclic compound binding nucleic acid binding	regulation of cellular process negative regulation of biological process 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 cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process 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 cellular 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 regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus cell communication cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway regulation of catalytic activity negative regulation of catalytic activity regulation of signal transduction regulation of transferase activity regulation of MAP kinase activity intracellular signal transduction negative regulation of kinase activity negative regulation of transferase activity negative regulation of JNK cascade regulation of phosphate metabolic process JNK cascade phosphate-containing compound metabolic process intracellular signaling cassette negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of JNK cascade regulation of MAPK cascade regulation of molecular function regulation of kinase activity regulation of response to stimulus negative regulation of protein phosphorylation regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphate metabolic process negative regulation of cell communication regulation of intracellular signal transduction negative regulation of protein serine/threonine kinase activity protein metabolic process negative regulation of JUN kinase activity regulation of signaling negative regulation of response to stimulus negative regulation of molecular function negative regulation of MAP kinase activity regulation of protein kinase activity negative regulation of protein kinase activity negative regulation of signal transduction negative regulation of phosphorus metabolic process regulation of JUN kinase activity MAPK cascade regulation of cell communication regulation of phosphorylation negative regulation of phosphorylation negative regulation of MAPK cascade regulation of defense response regulation of response to external stimulus defense response positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress response to stress positive regulation of defense response inflammatory response multicellular organismal process cellular developmental process heart morphogenesis cell development mesenchyme development epicardium-derived cardiac fibroblast cell differentiation multicellular organism development cardiac fibroblast cell development cell differentiation anatomical structure development cardiac epithelial to mesenchymal transition animal organ morphogenesis cardiac cell development system development developmental process heart development cardiac fibroblast cell differentiation animal organ development tissue development cardiocyte differentiation epithelial to mesenchymal transition involved in cardiac fibroblast development circulatory system development epithelial to mesenchymal transition anatomical structure morphogenesis epicardium-derived cardiac fibroblast cell development mesenchymal cell differentiation negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death positive regulation of apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process positive regulation of cellular process positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling response to chemical response to nitrogen compound response to alkaloid smooth muscle cell differentiation regulation of developmental process regulation of smooth muscle cell differentiation negative regulation of muscle cell differentiation regulation of cell differentiation muscle cell differentiation muscle structure development vascular associated smooth muscle cell differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of vascular associated smooth muscle cell differentiation regulation of vascular associated smooth muscle cell differentiation vasculature development negative regulation of smooth muscle cell differentiation regulation of muscle cell differentiation biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of myofibroblast differentiation myofibroblast differentiation negative regulation of myofibroblast differentiation muscle cell apoptotic process positive regulation of smooth muscle cell apoptotic process smooth muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of smooth muscle cell apoptotic process positive regulation of muscle cell apoptotic process vascular associated smooth muscle cell apoptotic process positive regulation of vascular associated smooth muscle cell apoptotic process regulation of vascular associated smooth muscle cell apoptotic process response to hormone regulation of vascular associated smooth muscle cell proliferation negative regulation of cell population proliferation cell population proliferation regulation of smooth muscle cell proliferation negative regulation of vascular associated smooth muscle cell proliferation smooth muscle cell proliferation negative regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation vascular associated smooth muscle cell proliferation regulation of cytokine production involved in inflammatory response cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response negative regulation of cytokine production cytokine production involved in inflammatory response negative regulation of gene expression negative regulation of multicellular organismal process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, D, F	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A, C, D, F	IPR044728	ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain	Domain
A, C, D, F	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
A, C, D, F	IPR011545	DEAD/DEAH box helicase domain	Domain
A, C, D, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, D, F	IPR001650	Helicase, C-terminal domain-like	Domain
A, C, D, F	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B, E	IPR016024	Armadillo-type fold	Homologous Superfamily
B, E	IPR039778	Programmed cell death protein 4	Family
B, E	IPR003891	Initiation factor eIF-4 gamma, MA3	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, D, F	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, E	Pharos: Q53EL6	Neoplasm Invasiveness cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma tuberculosis esophageal adenocarcinoma lung lymphangioleiomyomatosis lymphangioma malignant ependymoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia renal cell carcinoma Neoplasm Invasiveness cancer ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma tuberculosis esophageal adenocarcinoma lung lymphangioleiomyomatosis lymphangioma malignant ependymoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia renal cell carcinoma atrial fibrillation tuberous sclerosis lung adenocarcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor ulcerative colitis disappearing bone disease lung benign neoplasm malignant colon neoplasm

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.