4G0O

Crystal structure of Arabidopsis thaliana AGO5 MID domain

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	d4g0oa1	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4g0oa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4g0ob_	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	automated matches	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Mid domain of argonaute	8045671	4004605	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Mid domain of argonaute	8053597	3002210	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Mid domain of argonaute	8053597	3002210	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	Piwi_N_1	e4g0oA1	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: Piwi_N_1	ECOD (1.6)
B	Piwi_N_1	e4g0oB2	A: a/b three-layered sandwiches	X: Middle domain in Argonaute homologs (From Topology)	H: Middle domain in Argonaute homologs (From Topology)	T: Middle domain in Argonaute homologs	F: Piwi_N_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02171	Piwi domain (Piwi)	Piwi domain	-	Family
A, B	PF16487	Mid domain of argonaute (ArgoMid)	Mid domain of argonaute	The ArgoMid domain is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded beta-sheet core surrounded by four alpha-helices and two additional short alpha-helices. It most closely resembles the amino ...	The ArgoMid domain is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded beta-sheet core surrounded by four alpha-helices and two additional short alpha-helices. It most closely resembles the amino terminal tryptic core of the E.coli lactose repressor. There is an extensive interface between the Mid and the Piwi domains. The conserved C-terminal half or the Mid has extensive interactions with Piwi, with a deep basic pocket on the surface of the `Mid adjacent to the interface with Piwi. The Mid carries a binding pocket for the 5' phosphate overhang of the guide strand of DNA [1]. The N, Mid, and Piwi domains form a base upon which the PAZ domain sits, resembling a duck. The 5' phosphate and the U1 base are held in place by a conserved network of interactions from protein residues of the Mid and Piwi domains in order to place the guide uniquely in the proper position observed in all Argonaute-RNA complexes [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protein argonaute 5	RNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process response to stimulus negative regulation of biological process negative regulation of cellular metabolic process response to biotic stimulus post-transcriptional regulation of gene expression organic substance biosynthetic process response to virus RNAi-mediated antiviral immune response regulation of biological process immune response response to other organism cellular metabolic process negative regulation of metabolic process regulation of cellular process response to stimulus negative regulation of biological process negative regulation of cellular metabolic process response to biotic stimulus post-transcriptional regulation of gene expression organic substance biosynthetic process response to virus RNAi-mediated antiviral immune response regulation of biological process immune response response to other organism cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process response to external stimulus negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process defense response to other organism post-transcriptional gene silencing regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process biological process involved in interspecies interaction between organisms cellular biosynthetic process organic substance metabolic process response to stress negative regulation of cellular process innate immune response response to external biotic stimulus negative regulation of macromolecule metabolic process regulation of biosynthetic process defense response biological regulation defense response to symbiont regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing regulation of cellular biosynthetic process defense response to virus negative regulation of biosynthetic process immune system process cellular process organonitrogen compound biosynthetic process regulation of primary metabolic process protein metabolic process organonitrogen compound metabolic process regulation of protein metabolic process primary metabolic process translation regulation of translation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR045246	Argonaute-like, PIWI domain	Domain
A, B	IPR014811	Argonaute, linker 1 domain	Domain
A, B	IPR003100	PAZ domain	Domain
A, B	IPR032473	Protein argonaute, Mid domain	Domain
A, B	IPR032472	Argonaute linker 2 domain	Domain
A, B	IPR036085	PAZ domain superfamily	Homologous Superfamily
A, B	IPR003165	Piwi domain	Domain
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	IPR032474	Protein argonaute, N-terminal	Domain

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.