4NGC

Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having UA-3' ends (2.1 Angstrom resolution)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	PAZ	e4ngcA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
A	KOG0701	e4ngcA2	A: a+b two layers	X: Giardia Dicer N-terminal domain (From Topology)	H: Giardia Dicer N-terminal domain (From Topology)	T: Giardia Dicer N-terminal domain	F: KOG0701	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02170	PAZ domain (PAZ)	PAZ domain	This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel ...	This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved [2-4]. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.	Domain
A	PF20931	Dicer, platform domain (Dicer_platform)	Dicer, platform domain	This domain is found in Endoribonuclease Dicer from chordates. This dsRNA endoribonuclease is involved in the cleavage of long RNA precursors into short dsRNAs and plays a role in gene silencing. Dicer shows two N-terminal helicase domains (Pfam:PF04 ...	This domain is found in Endoribonuclease Dicer from chordates. This dsRNA endoribonuclease is involved in the cleavage of long RNA precursors into short dsRNAs and plays a role in gene silencing. Dicer shows two N-terminal helicase domains (Pfam:PF04851 and Pfam:PF00271), a dimerisation domain (Pfam:PF03368), a Platform domain, a PAZ domain (Pfam:PF02170), an RNase IIIa/b domain (Pfam:PF00636) and a dsRNA-binding domain in its C-terminal region. This entry represents the platform domain, which sits on the top of the L-shaped Dicer structure and shows a phosphate pocket [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Endoribonuclease Dicer	RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid 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 RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid 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 DNA binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity ribonuclease III activity double-stranded RNA-specific ribonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters cation binding metal ion binding helicase activity ATP-dependent activity protein binding protein domain specific binding regulatory RNA binding siRNA binding endodeoxyribonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity DNA endonuclease activity deoxyribonuclease I activity catalytic activity, acting on DNA pre-miRNA binding	regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process multicellular organismal process regulation of tumor necrosis factor production negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production regulation of multicellular organismal process tumor necrosis factor superfamily cytokine production negative regulation of cytokine production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production negative regulation of tumor necrosis factor superfamily cytokine production negative regulation of multicellular organismal process post-transcriptional regulation of gene expression global gene silencing by mRNA cleavage post-transcriptional gene silencing cellular developmental process peripheral nervous system axon ensheathment cellular component assembly involved in morphogenesis cell development glial cell development myelin assembly cellular component organization cellular component biogenesis multicellular organism development neurogenesis cellular anatomical entity morphogenesis cellular component assembly gliogenesis axon ensheathment ensheathment of neurons cell differentiation anatomical structure development myelination in peripheral nervous system cellular component organization or biogenesis Schwann cell differentiation system development developmental process peripheral nervous system development nervous system development peripheral nervous system myelin formation myelination anatomical structure morphogenesis Schwann cell development glial cell differentiation anatomical structure formation involved in morphogenesis ribonucleoprotein complex biogenesis RISC complex assembly protein-RNA complex assembly protein-RNA complex organization protein-containing complex assembly protein-containing complex organization nerve development regulation of primary metabolic process negative regulation of RNA biosynthetic process DNA-templated transcription 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 transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process pre-miRNA processing miRNA processing ncRNA metabolic process miRNA metabolic process positive regulation of nervous system development regulation of developmental process positive regulation of biological process regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of cellular process regulation of multicellular organismal development positive regulation of Schwann cell differentiation positive regulation of cell development regulation of glial cell differentiation positive regulation of glial cell differentiation regulation of Schwann cell differentiation positive regulation of multicellular organismal process cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization generation of neurons neuron development negative regulation of glial cell proliferation negative regulation of Schwann cell proliferation negative regulation of neurogenesis regulation of glial cell proliferation negative regulation of nervous system development negative regulation of cell differentiation Schwann cell proliferation negative regulation of cell population proliferation cell population proliferation regulation of Schwann cell proliferation negative regulation of developmental process negative regulation of gliogenesis negative regulation of cell development regulation of cell population proliferation glial cell proliferation system process regulation of myelination regulation of system process positive regulation of myelination positive regulation of nervous system process nervous system process regulation of nervous system process catabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process tRNA metabolic process nucleic acid catabolic process tRNA decay organic substance catabolic process RNA catabolic process execution phase of apoptosis DNA catabolic process apoptotic nuclear changes cellular component disassembly DNA metabolic process cell death apoptotic DNA fragmentation cellular component disassembly involved in execution phase of apoptosis apoptotic process programmed cell death cellular response to stimulus response to organic substance response to stimulus negative regulation of signaling signaling response to cytokine regulation of signal transduction negative regulation of cell communication cytokine-mediated signaling pathway cell communication cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction cellular response to organic substance regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway negative regulation of response to stimulus regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway negative regulation of signal transduction regulation of response to cytokine stimulus cellular response to chemical stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus negative regulation of cytokine-mediated signaling pathway response to chemical regulation of cell communication response to tumor necrosis factor	protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm RISC-loading complex endoribonuclease complex catalytic complex intracellular protein-containing complex endonuclease complex intracellular organelle nucleus intracellular membrane-bounded organelle
B	5'-R(GPCPGPAPAPUPUPCPGPCPUPA)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR048513	Dicer, partner-binding domain	Domain
A	IPR044441	Dicer, double-stranded RNA-binding domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR006935	Helicase/UvrB, N-terminal	Domain
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR005034	Dicer dimerisation domain	Domain
A	IPR038248	Dicer dimerisation domain superfamily	Homologous Superfamily
A	IPR000999	Ribonuclease III domain	Domain
A	IPR003100	PAZ domain	Domain
A	IPR048512	Dicer, platform domain	Domain
A	IPR036389	Ribonuclease III, endonuclease domain superfamily	Homologous Superfamily
A	IPR036085	PAZ domain superfamily	Homologous Superfamily
A	IPR014720	Double-stranded RNA-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UPY3	pleuropulmonary blastoma endometriosis Rhabdomyosarcoma, embryonal, 2 kidney Wilms tumor oligospermia cancer goiter, multinodular 1, with or without Sertoli-Leydig cell tumors Sertoli cell tumor hepatocellular carcinoma thyroid gland carcinoma juvenile dermatomyositis liver cancer multinodular goiter adrenal cortex carcinoma osteosarcoma pleuropulmonary blastoma endometriosis Rhabdomyosarcoma, embryonal, 2 kidney Wilms tumor oligospermia cancer goiter, multinodular 1, with or without Sertoli-Leydig cell tumors Sertoli cell tumor hepatocellular carcinoma thyroid gland carcinoma juvenile dermatomyositis liver cancer multinodular goiter adrenal cortex carcinoma osteosarcoma astrocytic tumor ovarian Sertoli-Leydig cell tumor pituitary gland adenoma Crohn disease primitive neuroectodermal tumor rhabdomyosarcoma Gaucher disease sarcoidosis Sertoli-Leydig cell tumor hereditary spastic paraplegia tuberculosis lymphoplasmacytic lymphoma malignant mesothelioma myopathy Alzheimer disease ovarian cancer atrial fibrillation pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer plasma cell myeloma dermatomyositis progressive supranuclear palsy glioblastoma schizophrenia granulosa cell tumor sex cord-stromal tumor IgA glomerulonephritis ulcerative colitis large cell medulloblastoma medulloblastoma amyotrophic lateral sclerosis ovarian gynandroblastoma atypical teratoid rhabdoid tumor Pick disease psoriasis rheumatoid arthritis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.