6L5M

Crystal structure of human DEAD-box RNA helicase DDX21 in complex with AMP

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DEAD	e6l5mA2	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	e6l5mA1	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	e6l5mB2	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	e6l5mB1	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	e6l5mC2	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	e6l5mC1	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	e6l5mD2	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	e6l5mD1	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	DEAD	e6l5mE2	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)
E	Helicase_C_1	e6l5mE1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	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, C, D, E	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
A, B, C, D, E	Nucleolar RNA helicase 2	RNA binding binding organic cyclic compound binding snoRNA binding nucleic acid binding double-stranded RNA binding rRNA binding snRNA binding 7SK snRNA binding regulatory RNA binding miRNA binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding RNA binding binding organic cyclic compound binding snoRNA binding nucleic acid binding double-stranded RNA binding rRNA binding snRNA binding 7SK snRNA binding regulatory RNA binding miRNA 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 ATP-dependent activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA enzyme regulator activity RNA polymerase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity identical protein binding protein binding	developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling developmental process multicellular organismal process cellular developmental process ossification cell differentiation cellular process osteoblast differentiation cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis R-loop processing cellular biosynthetic process cellular metabolic 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 transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process response to chemical response to dsRNA response to nitrogen compound response to exogenous dsRNA response to organic cyclic compound biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis RNA processing rRNA metabolic process regulation of immune effector process positive regulation of leukocyte mediated immunity regulation of myeloid leukocyte mediated immunity positive regulation of macromolecule biosynthetic process myeloid leukocyte mediated immunity positive regulation of metabolic process dendritic cell cytokine production cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of immune system process regulation of cytokine production involved in immune response regulation of cellular metabolic process immune effector process regulation of gene expression regulation of leukocyte mediated immunity myeloid dendritic cell cytokine production positive regulation of myeloid leukocyte mediated immunity positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of dendritic cell cytokine production positive regulation of cellular metabolic process regulation of myeloid dendritic cell cytokine production positive regulation of biosynthetic process positive regulation of myeloid leukocyte cytokine production involved in immune response regulation of dendritic cell cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of immune effector process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process positive regulation of myeloid dendritic cell cytokine production positive regulation of gene expression positive regulation of cytokine production involved in immune response positive regulation of cellular biosynthetic process positive regulation of DNA-templated transcription regulation of primary metabolic process regulation of RNA metabolic process transcription by RNA polymerase I regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase I regulation of RNA biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase III transcription by RNA polymerase III regulation of transcription by RNA polymerase III defense response to virus response to virus regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II negative regulation of biological process negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase I negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane cytosol nucleoplasm chromosome ATPase complex protein-containing complex catalytic complex B-WICH complex nuclear protein-containing complex chromatin SWI/SNF superfamily-type complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B, C, D, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E	IPR001650	Helicase, C-terminal domain-like	Domain
A, B, C, D, E	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B, C, D, E	IPR012562	GUCT	Domain
A, B, C, D, E	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: Q9NR30	congestive heart failure juvenile dermatomyositis malignant colon neoplasm ovarian cancer Sjogren syndrome dermatomyositis large cell medulloblastoma medulloblastoma plasma cell myeloma ulcerative colitis diabetes mellitus lung cancer myopathy psoriasis

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.