7W84 | pdb_00007w84

CryoEM structure of apo form ZmRDR2 at 3.4 Angstroms resolution

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05183	RNA dependent RNA polymerase (RdRP)	RNA dependent RNA polymerase	-	Family
A	PF26253	RdRP, head domain (RdRP_head)	RdRP, head domain	This domain is found C-terminal in the RNA-dependent RNA polymerases such as RDR1/2/3/4/5/6 and related proteins. This domain folds into array of alpha helices and it is known as head [1]. The head domain was proposed to interact with incoming templa ...	This domain is found C-terminal in the RNA-dependent RNA polymerases such as RDR1/2/3/4/5/6 and related proteins. This domain folds into array of alpha helices and it is known as head [1]. The head domain was proposed to interact with incoming template RNA, helping guide the RNA to the active site [1].	Domain
A	PF26252	RNA dependent RNA polymerase, helical domain (RdRP_helical)	RNA dependent RNA polymerase, helical domain	This domain is found in eukaryotic RNA dependent RNA polymerases. It folds into array of helices [1].	Domain
A	PF24823	RDR2 PH-like domain (PH_RDR2)	RDR2 PH-like domain	This domain is found in RNA-dependent RNA polymerase 2 (RDR2) from Arabidopsis thaliana and related proteins. RDR2 is involved in the production of small interfering RNAs (siRNAs). It binds to single-stranded RNA (ssRNA), engages ssRNAs longer than 7 ...	This domain is found in RNA-dependent RNA polymerase 2 (RDR2) from Arabidopsis thaliana and related proteins. RDR2 is involved in the production of small interfering RNAs (siRNAs). It binds to single-stranded RNA (ssRNA), engages ssRNAs longer than 7 nucleotides and initiates internal to their 3' ends [1]. RDR2 is non-functional in the absence of associated Pol IV [2]. The domain represented by this entry adopts a beta-barrel structure with significant similarity to known PH domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RNA-dependent RNA polymerase	RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding	regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular process negative regulation of biological process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression 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 cellular component organization cellular component biogenesis siRNA-mediated heterochromatin formation cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression heterochromatin organization constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation DNA methylation-dependent constitutive heterochromatin formation negative regulation of gene expression, epigenetic gene silencing by siRNA-directed DNA methylation retrotransposition transposable element silencing by heterochromatin formation transposition transposable element silencing by siRNA-mediated heterochromatin formation transposable element silencing	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus RNA-directed RNA polymerase complex nuclear protein-containing complex nuclear RNA-directed RNA polymerase complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus RNA-directed RNA polymerase complex nuclear protein-containing complex nuclear RNA-directed RNA polymerase complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle RNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR057590	RDR1/2-like, PH-like domain	Domain
A	IPR000504	RNA recognition motif domain	Domain
A	IPR057596	RDRP, core domain	Domain
A	IPR058751	RDRP, helical domain	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR058752	RDRP, C-terminal head domain	Domain
A	IPR007855	RNA-dependent RNA polymerase	Family
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A	IPR058763	RDR1/2-like, RRM domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.