1YTY

Structural basis for recognition of UUUOH 3'-terminii of nascent RNA pol III transcripts by La autoantigen

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)
C [auth A]	d1ytya1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	La domain	Lupus La autoantigen N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1ytya2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Lupus LA protein	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d1ytyb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	La domain	Lupus La autoantigen N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d1ytyb2	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	Canonical RBD	Lupus LA protein	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)
C [auth A]	SCOP2B Superfamily	RNA-binding domain, RBD	8003167	3000110	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003164	3000034	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003164	3000034	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	RNA-binding domain, RBD	8003167	3000110	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 A]	La	e1ytyA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: La	ECOD (1.6)
C [auth A]	RRM_1_1	e1ytyA2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)
D [auth B]	La	e1ytyB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: La	ECOD (1.6)
D [auth B]	RRM_1_1	e1ytyB2	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C [auth A]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
D [auth B]	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D [auth B]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF05383	La domain (La)	La domain	This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins [1]. The function of this region is uncertain.	Domain
C [auth A], D [auth B]	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	5'-R(UPGPCPUPGPUPUPUP*U)-3'	-	-	-
C [auth A], D [auth B]	Lupus La protein	RNA binding binding nucleic acid binding tRNA binding sequence-specific mRNA binding mRNA binding poly-pyrimidine tract binding poly(U) RNA binding single-stranded RNA binding	cellular localization RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport nucleic acid transport intracellular transport tRNA export from nucleus establishment of localization RNA export from nucleus localization tRNA transport establishment of RNA localization establishment of localization in cell cellular localization RNA transport nitrogen compound transport nucleocytoplasmic transport transport nuclear transport nucleic acid transport intracellular transport tRNA export from nucleus establishment of localization RNA export from nucleus localization tRNA transport establishment of RNA localization establishment of localization in cell macromolecule localization cellular process RNA localization nuclear export nucleobase-containing compound transport RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process tRNA processing metabolic process macromolecule metabolic process RNA processing tRNA modification RNA modification macromolecule modification regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process RNA 5'-end processing tRNA 5'-leader removal tRNA 5'-end processing histone mRNA metabolic process mRNA metabolic process catabolic process negative regulation of biological process macromolecule catabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process histone mRNA catabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression nuclear histone mRNA catabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process viral gene expression viral process viral translation IRES-dependent viral translational initiation protein localization protein localization to cytoplasmic stress granule protein localization to organelle cellular macromolecule localization RNA 3'-end processing tRNA 3'-end processing	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol protein-containing complex ribonucleoprotein complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cytosol protein-containing complex ribonucleoprotein complex chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR002344	Lupus La protein	Family
C [auth A], D [auth B]	IPR006630	La-type HTH domain	Domain
C [auth A], D [auth B]	IPR014886	La protein, xRRM domain	Domain
C [auth A], D [auth B]	IPR000504	RNA recognition motif domain	Domain
C [auth A], D [auth B]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR045180	La domain containing protein	Family
C [auth A], D [auth B]	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], D [auth B]	Pharos: P05455	atrioventricular block lung adenocarcinoma myopathy Potocki-Shaffer syndrome Sjogren syndrome gastric carcinoma lung cancer osteosarcoma progressive supranuclear palsy juvenile dermatomyositis lupus erythematosus ovarian cancer psoriasis

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.