1SI2

Crystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like duplex of deoxynucleotide overhang

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)
B [auth A]	d1si2a1	All beta proteins	SH3-like barrel	PAZ domain	PAZ domain	Eukaryotic translation initiation factor 2C 1, EIF2C1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d1si2a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
B [auth A]	SCOP2B Superfamily	PAZ domain	8053607	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)
B [auth A]	PAZ	e1si2A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PAZ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	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
B [auth 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	5'-R(CPGPUPGPAPCPU)-D(PCP*T)-3'	-	-	-
B [auth A]	Eukaryotic translation initiation factor 2C 1	RNA binding double-stranded RNA binding binding nucleic acid binding single-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 regulatory RNA binding miRNA binding RNA binding double-stranded RNA binding binding nucleic acid binding single-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 regulatory RNA 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 catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality regulation of catabolic process regulation of mRNA stability regulation of RNA stability regulation of mRNA metabolic process regulatory ncRNA-mediated post-transcriptional gene silencing regulatory ncRNA-mediated gene silencing post-transcriptional gene silencing pre-miRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing nucleobase-containing compound biosynthetic process regulatory ncRNA processing miRNA processing negative regulation of translation miRNA-mediated gene silencing by inhibition of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation miRNA-mediated post-transcriptional gene silencing regulation of translation ribonucleoprotein complex biogenesis RISC complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization multicellular organismal process regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle protein-containing complex ribonucleoprotein complex RNAi effector complex RISC complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A]	Pharos: Q9UL18	malignant mesothelioma Alcoholic Intoxication, Chronic lung cancer depressive disorder pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia intellectual disability medulloblastoma Pick disease

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.