4A4D | pdb_00004a4d

Crystal structure of the N-terminal domain of the Human DEAD-BOX RNA helicase DDX5 (P68)

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	d4a4da_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	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	8068443	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)
A	DEAD	e4a4dA1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROBABLE ATP-DEPENDENT RNA HELICASE DDX5	SMAD binding protein binding binding R-SMAD binding RNA binding primary miRNA binding nucleic acid binding mRNA 3'-UTR binding mRNA binding chromatin binding promoter-specific chromatin binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding SMAD binding protein binding binding R-SMAD binding RNA binding primary miRNA binding nucleic acid binding mRNA 3'-UTR binding mRNA binding chromatin binding promoter-specific chromatin 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 calmodulin binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity catalytic activity ATP-dependent activity pre-mRNA binding ribonucleoprotein complex binding protein-containing complex binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding nuclear androgen receptor binding MH2 domain binding protein domain specific 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 calcium-dependent protein binding enzyme binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process miRNA transcription biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process miRNA transcription biosynthetic process metabolic process cellular process macromolecule metabolic process miRNA metabolic process regulation of cellular process catabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process mRNA metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development myoblast differentiation cellular response to stimulus intracellular receptor signaling pathway response to stimulus response to lipid signaling hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone androgen receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway signal transduction by p53 class mediator cell death apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator apoptotic process intrinsic apoptotic signaling pathway programmed cell death skeletal muscle cell differentiation regulation of developmental process skeletal muscle tissue development animal organ development regulation of cell differentiation tissue development striated muscle tissue development skeletal muscle organ development regulation of skeletal muscle cell differentiation muscle tissue development muscle organ development mRNA transcription positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress positive regulation of biological process regulation of signal transduction DNA damage response, signal transduction by p53 class mediator positive regulation of response to stimulus cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of cellular process regulation of signaling positive regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of intracellular signal transduction regulation of response to stimulus DNA damage response regulation of cell communication signal transduction in response to DNA damage positive regulation of signaling mesenchyme development mesenchymal cell differentiation epithelial to mesenchymal transition estrogen receptor signaling pathway regulation of primary metabolic process negative regulation of RNA 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA splicing alternative mRNA splicing, via spliceosome mRNA processing RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing regulation of osteoblast differentiation multicellular organismal process osteoblast differentiation ossification 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 BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway regulation of mRNA splicing, via spliceosome regulation of mRNA processing regulation of RNA splicing regulation of alternative mRNA splicing, via spliceosome regulation of mRNA metabolic process rhythmic process regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication viral life cycle regulatory ncRNA processing regulatory ncRNA-mediated gene silencing primary miRNA processing miRNA processing regulation of intracellular steroid hormone receptor signaling pathway regulation of androgen receptor signaling pathway	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol nucleolus catalytic step 2 spliceosome protein-containing complex catalytic complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012587	RNA helicase p68 repeat	Repeat
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
A	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P17844	endometriosis atypical teratoid rhabdoid tumor ovarian cancer diabetes mellitus glioblastoma subependymal giant cell astrocytoma Endometrioma non-small cell lung carcinoma

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.