4OLB

Crystal Structure of Human Argonaute2 Bound to Tryptophan

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	d4olba1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	Argonaute 2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4olba2	Alpha and beta proteins (a/b)	Phosphotyrosine protein phosphatases I-like	PIWI domain N-terminal-like	PIWI domain N-terminal	Argonaute-2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4olba3	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	PIWI domain C-terminal	Argonaute-2	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	Mid domain of argonaute	8053594	3002210	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8053661	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RNA-binding domain, RBD	8053657	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PAZ domain	8053659	3001750	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	PAZ	e4olbA8	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
A	ArgoN	e4olbA9	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: ArgoN	ECOD (1.6)
A	ArgoL1	e4olbA10	A: a+b two layers	X: Alpha-beta plaits	H: Argonaute, N-terminal domain (From Topology)	T: Argonaute, N-terminal domain	F: ArgoL1	ECOD (1.6)
A	Piwi_N_1	e4olbA7	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)
A	Piwi_C	e4olbA6	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Piwi_C	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)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF02171	Piwi domain (Piwi)	Piwi domain	-	Family
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	PF16486	N-terminal domain of argonaute (ArgoN)	N-terminal domain of argonaute	ArgoN is the N-terminal domain of argonaute proteins in eukaryotes. ArgoN is composed of an antiparallel four-stranded beta sheet core that has two alpha helices positioned along one face of the sheet and an extended beta strand towards its N-terminu ...	ArgoN is the N-terminal domain of argonaute proteins in eukaryotes. ArgoN is composed of an antiparallel four-stranded beta sheet core that has two alpha helices positioned along one face of the sheet and an extended beta strand towards its N-terminus. The core fold of the N domain most closely resembles the catalytic domain of replication-initiator protein Rep. The N domain is linked to the PAZ domain via linker 1 region, and together these three regions are designated the PAZ-containing lobe of argonaute.	Domain
A	PF16488	Argonaute linker 2 domain (ArgoL2)	Argonaute linker 2 domain	-	Family
A	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
A	PF08699	Argonaute linker 1 domain (ArgoL1)	Argonaute linker 1 domain	ArgoL1 is a region found in argonaute [1] proteins. It normally co-occurs with Pfam:PF02179 and Pfam:PF02171. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel be ...	ArgoL1 is a region found in argonaute [1] proteins. It normally co-occurs with Pfam:PF02179 and Pfam:PF02171. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel beta-sheet with two long beta-strands (beta8 and beta9) of the sheet spanning one face of the adjacent N and PAZ domains. L1 together with linker 2, L2, PAZ and ArgoN forms a compact global fold [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein argonaute-2	translation factor activity translation initiation factor activity translation factor activity, RNA binding RNA binding mRNA cap binding binding nucleic acid binding RNA cap binding mRNA binding double-stranded RNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding translation factor activity translation initiation factor activity translation factor activity, RNA binding RNA binding mRNA cap binding binding nucleic acid binding RNA cap binding mRNA binding double-stranded RNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding core promoter sequence-specific DNA binding transcription regulatory region nucleic acid binding RNA 7-methylguanosine cap 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 RNA endonuclease activity, producing 5'-phosphomonoesters endoribonuclease activity, cleaving siRNA-paired mRNA endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters cation binding ion binding metal ion binding small molecule binding endoribonuclease activity, cleaving miRNA-paired mRNA regulatory RNA binding siRNA binding single-stranded RNA binding mRNA 3'-UTR binding mRNA 3'-UTR AU-rich region binding miRNA binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme 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 regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay nucleobase-containing compound catabolic process positive regulation of RNA metabolic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process macromolecule catabolic process mRNA destabilization regulation of mRNA catabolic process regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of cellular process RNA destabilization nuclear-transcribed mRNA catabolic process regulation of catabolic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process post-transcriptional gene silencing siRNA-mediated gene silencing by mRNA destabilization siRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated post-transcriptional gene silencing cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly membraneless organelle assembly cellular component organization or biogenesis developmental process multicellular organismal process regulation of cellular component organization regulation of developmental process nervous system development developmental maturation synapse maturation regulation of synapse organization multicellular organism development regulation of synapse maturation cell junction organization anatomical structure development regulation of synapse structure or activity synapse organization system development ribonucleoprotein complex biogenesis RISC complex assembly protein-RNA complex assembly protein-RNA complex organization protein-containing complex assembly protein-containing complex organization negative regulation of translation translational initiation protein metabolic process negative regulation of protein metabolic process regulation of translational initiation regulation of protein metabolic process negative regulation of translational initiation translation regulation of translation multi-multicellular organism process positive regulation of locomotion regulation of cell motility regulation of trophoblast cell migration regulation of reproductive process reproductive process positive regulation of cell migration positive regulation of developmental process ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration regulation of multicellular organismal process cell motility female pregnancy embryo implantation locomotion positive regulation of reproductive process trophoblast cell migration positive regulation of trophoblast cell migration regulation of locomotion positive regulation of multicellular organismal process multi-organism reproductive process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic process regulation of DNA-templated transcription pre-miRNA processing miRNA processing miRNA metabolic process carbohydrate derivative metabolic process amyloid precursor protein biosynthetic process negative regulation of amyloid precursor protein biosynthetic process regulation of amyloid precursor protein biosynthetic process amyloid precursor protein metabolic process regulation of glycoprotein biosynthetic process carbohydrate derivative biosynthetic process negative regulation of glycoprotein biosynthetic process negative regulation of glycoprotein metabolic process glycoprotein biosynthetic process glycoprotein metabolic process regulation of glycoprotein metabolic process miRNA-mediated gene silencing by inhibition of translation miRNA-mediated post-transcriptional gene silencing miRNA-mediated gene silencing by mRNA destabilization positive regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening positive regulation of protein metabolic process positive regulation of translation positive regulation of gene expression angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis post-embryonic development	protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse postsynapse nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen nuclear lumen membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle supramolecular complex ribonucleoprotein granule RISC-loading complex endoribonuclease complex catalytic complex intracellular protein-containing complex endonuclease complex P-body
B	5'-R(PAPAPAPAPAPAPAPAPAPU)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR014811	Argonaute, linker 1 domain	Domain
A	IPR032472	Argonaute linker 2 domain	Domain
A	IPR045246	Argonaute-like, PIWI domain	Domain
A	IPR003165	Piwi domain	Domain
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR003100	PAZ domain	Domain
A	IPR028602	Protein argonaute-2	Family
A	IPR032473	Protein argonaute, Mid domain	Domain
A	IPR036085	PAZ domain superfamily	Homologous Superfamily
A	IPR032474	Protein argonaute, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UKV8	myeloid leukemia malignant mesothelioma cocaine dependence chronic monocytic leukemia cocaine abuse myopathy osteosarcoma pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis Alcoholic Intoxication, Chronic tuberculosis attention deficit hyperactivity disorder, inattentive type cancer glioblastoma malignant ependymoma myeloid leukemia malignant mesothelioma cocaine dependence chronic monocytic leukemia cocaine abuse myopathy osteosarcoma pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis Alcoholic Intoxication, Chronic tuberculosis attention deficit hyperactivity disorder, inattentive type cancer glioblastoma malignant ependymoma medulloblastoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma Pick disease spina bifida astrocytic tumor X-linked mixed deafness with perilymphatic gusher atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor subependymal giant cell astrocytoma atrial fibrillation breast cancer diabetes mellitus lung cancer

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.