2VSO | pdb_00002vso

Crystal Structure of a Translation Initiation 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2vsoa1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d2vsob1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	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	8044315	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8044315	3002019	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)
D [auth F]	MIF4G	e2vsoF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MIF4G	ECOD (1.6)
C [auth E]	MIF4G	e2vsoE2	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: MIF4G	ECOD (1.6)
A	DEAD	e2vsoA1	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	e2vsoA2	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)
B	DEAD	e2vsoB1	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)
B	Helicase_C_1	e2vsoB2	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)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth E], D [auth F]	PF02854	MIF4G domain (MIF4G)	MIF4G domain	-	Repeat
A, B	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, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F]	EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150	translation factor activity translation initiation factor activity RNA binding binding nucleic acid binding mRNA binding ATPase activator activity molecular function activator activity molecular function regulator activity ATPase regulator activity molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular process protein metabolic process macromolecule metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular process protein metabolic process macromolecule metabolic process cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis ribosomal large subunit biogenesis regulation of cellular process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of biological process regulation of translational initiation regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to glucose starvation cellular response to starvation cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly protein-RNA complex organization regulation of cytoplasmic translation regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process protein-RNA complex assembly regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of formation of translation preinitiation complex protein-containing complex assembly formation of translation preinitiation complex positive regulation of cellular process protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of formation of translation preinitiation complex regulation of cytoplasmic translational initiation cytoplasmic translation cytoplasmic translational initiation positive regulation of cell communication positive regulation of signal transduction signaling regulation of cellular response to stress endoplasmic reticulum unfolded protein response regulation of response to endoplasmic reticulum stress regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of endoplasmic reticulum unfolded protein response positive regulation of response to endoplasmic reticulum stress regulation of intracellular signal transduction regulation of response to stress positive regulation of endoplasmic reticulum unfolded protein response signal transduction response to endoplasmic reticulum stress regulation of signaling cellular response to topologically incorrect protein positive regulation of intracellular signal transduction cellular response to unfolded protein response to unfolded protein regulation of response to stimulus response to topologically incorrect protein regulation of cell communication positive regulation of signaling	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule P-body protein-containing complex eukaryotic translation initiation factor 4F complex RNA cap binding complex intracellular protein-containing complex ribosome
A, B	ATP-DEPENDENT RNA HELICASE EIF4A	translation factor activity translation initiation factor activity 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 translation factor activity translation initiation factor activity 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 ATP-dependent activity, acting on RNA ATP-dependent 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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity macromolecular conformation isomerase activity RNA binding nucleic acid binding	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of cellular process regulation of primary metabolic process post-transcriptional regulation of gene expression primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process translational initiation metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of cellular process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of biological process regulation of translational initiation regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process cytoplasmic translation cytoplasmic translational initiation ribonucleoprotein complex biogenesis cellular component biogenesis protein-RNA complex organization cellular component assembly regulation of cytoplasmic translation regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process protein-RNA complex assembly cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of formation of translation preinitiation complex protein-containing complex assembly cellular component organization or biogenesis formation of translation preinitiation complex positive regulation of cellular process protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis regulation of formation of translation preinitiation complex regulation of cytoplasmic translational initiation	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cell periphery plasma membrane membrane intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cell periphery plasma membrane membrane protein-containing complex eukaryotic translation initiation factor 4F complex RNA cap binding complex intracellular protein-containing complex ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], D [auth F]	IPR036211	eIF4G, eIF4e-binding domain superfamily	Homologous Superfamily
C [auth E], D [auth F]	IPR016024	Armadillo-type fold	Homologous Superfamily
C [auth E], D [auth F]	IPR022745	Eukaryotic translation initiation factor 4G1, eIF4E-binding domain	Domain
C [auth E], D [auth F]	IPR003890	MIF4G-like, type 3	Domain
A, B	IPR001650	Helicase, C-terminal domain-like	Domain
A, B	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A, B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B	IPR044728	ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain	Domain
A, B	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
A, B	IPR011545	DEAD/DEAH-box helicase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.