5JS2

Human Argonaute-2 Bound to a Modified siRNA


ChainDomainClassArchitectureTopologyHomology
A2.170.260.10 Mainly Beta Beta Complex paz domain paz domain
A3.40.50.2300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Response regulator
A3.30.420.10 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
APF02171Piwi domain (Piwi)Piwi domain- Family
APF02170PAZ domain (PAZ)PAZ domainThis 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
APF16486N-terminal domain of argonaute (ArgoN)N-terminal domain of argonauteArgoN 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
APF16488Argonaute linker 2 domain (ArgoL2)Argonaute linker 2 domain- Family
APF16487Mid domain of argonaute (ArgoMid)Mid domain of argonauteThe 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
APF08699Argonaute linker 1 domain (ArgoL1)Argonaute linker 1 domainArgoL1 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 Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
AProtein argonaute-2
Bmodified siRNAnone none none