1R6Z | pdb_00001r6z

The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion)

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)
C [auth Z]	d1r6zz1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	Argonaute 2	, fruit fly (Escherichia coli ) [TaxId: 562 ], , fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C [auth Z]	d1r6zz2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	D-maltodextrin-binding protein, MBP	, fruit fly (Escherichia coli ) [TaxId: 562 ], , fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B [auth A]	d1r6za1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	Argonaute 2	, fruit fly (Escherichia coli ) [TaxId: 562 ], , fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B [auth A]	d1r6za2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	D-maltodextrin-binding protein, MBP	, fruit fly (Escherichia coli ) [TaxId: 562 ], , fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A [auth P]	d1r6zp1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	Argonaute 2	, fruit fly (Escherichia coli ) [TaxId: 562 ], , fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
A [auth P]	d1r6zp2	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	D-maltodextrin-binding protein, MBP	, fruit fly (Escherichia coli ) [TaxId: 562 ], , fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth Z]	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
C [auth Z]	SCOP2B Superfamily	PAZ domain	8041535	3001750	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	PAZ domain	8041535	3001750	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	PAZ domain	8041535	3001750	SCOP2B (2022-06-29)
A [auth P]	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	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)
C [auth Z]	PAZ	e1r6zZ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
C [auth Z]	SBP_bac_1_C	e1r6zZ3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
C [auth Z]	SBP_bac_1_N_1	e1r6zZ2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
B [auth A]	PAZ	e1r6zA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
B [auth A]	SBP_bac_1_C	e1r6zA3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B [auth A]	SBP_bac_1_N_1	e1r6zA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
A [auth P]	PAZ	e1r6zP1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)
A [auth P]	SBP_bac_1_C	e1r6zP2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
A [auth P]	SBP_bac_1_N_1	e1r6zP3	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth Z]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C [auth Z]	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)
B [auth A]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B [auth A]	2.170.260.10	Mainly Beta	Beta Complex	paz domain	paz domain	CATH (4.3.0)
A [auth P]	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A [auth P]	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 [auth P], B [auth A], C [auth Z]	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A [auth P], B [auth A], C [auth Z]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], B [auth A], C [auth Z]	Chimera of Maltose-binding periplasmic protein and Argonaute 2	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding regulatory RNA binding RNA binding siRNA binding nucleic acid binding single-stranded RNA binding miRNA binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding regulatory RNA binding RNA binding siRNA binding nucleic acid binding single-stranded RNA binding miRNA binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism hydrolase activity hydrolase activity, acting on ester bonds endoribonuclease activity, cleaving siRNA-paired mRNA cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus regulation of biosynthetic process regulation of biological process regulation of cellular process sex-chromosome dosage compensation epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process cellular component organization regulation of gene expression biosynthetic process dosage compensation by hyperactivation of X chromosome chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular component organization or biogenesis macromolecule metabolic process regulation of metabolic 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 negative regulation of metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process biological process involved in interspecies interaction between organisms response to biotic stimulus post-transcriptional regulation of gene expression innate immune response response to external biotic stimulus response to virus RNAi-mediated antiviral immune response immune response response to other organism defense response defense response to symbiont regulatory ncRNA-mediated post-transcriptional gene silencing defense response to virus immune system process defense response to other organism post-transcriptional gene silencing developmental process multicellular organismal process blastoderm segmentation embryonic pattern specification segmentation pattern specification process embryo development regionalization multicellular organism development anatomical structure development segment polarity determination periodic partitioning regulation of primary metabolic process positive regulation of metabolic process 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 mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process nucleic acid catabolic process catabolic process positive regulation of biological process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process positive regulation of cellular process RNA destabilization 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 piRNA-mediated gene silencing by mRNA destabilization regulation of mRNA metabolic process siRNA-mediated gene silencing by mRNA destabilization siRNA-mediated post-transcriptional gene silencing establishment of organelle localization cellular localization nucleus localization intracellular transport embryonic development via the syncytial blastoderm embryo development ending in birth or egg hatching organelle localization establishment of localization in cell syncytial nuclear migration nuclear migration cellular component biogenesis siRNA-mediated heterochromatin formation cellular component assembly heterochromatin formation siRNA-mediated pericentric heterochromatin formation heterochromatin organization pericentric heterochromatin formation constitutive heterochromatin formation regulatory ncRNA-mediated heterochromatin formation negative regulation of gene expression, epigenetic 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 viral genome replication viral life cycle negative regulation of viral process regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication RNAi-mediated antiviral immunity against RNA virus piRNA processing sexual reproduction cellular developmental process reproductive process cellularization multicellular organismal reproductive process cell development pole cell formation developmental process involved in reproduction gamete generation anatomical structure morphogenesis pole cell development cell differentiation anatomical structure formation involved in morphogenesis miRNA-mediated post-transcriptional gene silencing cellular response to virus	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope ribonucleoprotein complex RNAi effector complex RISC complex intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle supramolecular complex ribonucleoprotein granule neuron projection cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection cell projection neuronal ribonucleoprotein granule RISC-loading complex endoribonuclease complex catalytic complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth P], B [auth A], C [auth Z]	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A [auth P], B [auth A], C [auth Z]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A [auth P], B [auth A], C [auth Z]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A [auth P], B [auth A], C [auth Z]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A [auth P], B [auth A], C [auth Z]	IPR014811	Argonaute, linker 1 domain	Domain
A [auth P], B [auth A], C [auth Z]	IPR032472	Argonaute linker 2 domain	Domain
A [auth P], B [auth A], C [auth Z]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A [auth P], B [auth A], C [auth Z]	IPR045246	Argonaute-like, PIWI domain	Domain
A [auth P], B [auth A], C [auth Z]	IPR003100	PAZ domain	Domain
A [auth P], B [auth A], C [auth Z]	IPR032473	Protein argonaute, Mid domain	Domain
A [auth P], B [auth A], C [auth Z]	IPR036085	PAZ domain superfamily	Homologous Superfamily
A [auth P], B [auth A], C [auth Z]	IPR003165	Piwi domain	Domain
A [auth P], B [auth A], C [auth Z]	IPR032474	Protein argonaute, N-terminal	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.