2VOD

Crystal structure of N-terminal domains of Human La protein complexed with RNA oligomer AUAUUUU

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2voda1	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)
A	d2voda2	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)
B	d2vodb1	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)
B	d2vodb2	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)
A	SCOP2B Superfamily	RNA-binding domain RBD	8003167	3000110	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8003164	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8003164	3000034	SCOP2B (2022-06-29)
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)
A	La	e2vodA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: La	ECOD (1.6)
A	RRM_1_1	e2vodA2	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)
B	La	e2vodB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: La	ECOD (1.6)
B	RRM_1_1	e2vodB2	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)
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)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)
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)
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
A, 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
A, 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, B	LUPUS LA PROTEIN	RNA binding binding organic cyclic compound 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 organic substance 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 cellular localization RNA transport nitrogen compound transport nucleocytoplasmic transport transport organic substance 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 macromolecule localization establishment of localization in cell cellular process RNA localization ncRNA export from nucleus nucleobase-containing compound transport nuclear export cellular biosynthetic process RNA metabolic process ncRNA processing nucleobase-containing compound metabolic process organic substance metabolic process heterocycle metabolic process tRNA processing organic substance biosynthetic process nitrogen compound metabolic process RNA processing cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process organic cyclic compound metabolic process biosynthetic process ncRNA metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process cellular aromatic compound metabolic process tRNA modification RNA modification macromolecule modification regulation of cellular process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process regulation of nitrogen compound 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 organonitrogen compound metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process translation regulation of cellular biosynthetic process regulation of gene expression positive regulation of nitrogen compound metabolic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process tRNA 5'-end processing RNA 5'-end processing tRNA 5'-leader removal histone mRNA metabolic process mRNA metabolic process negative regulation of biological process negative regulation of cellular metabolic process cellular catabolic process RNA catabolic process mRNA catabolic process negative regulation of metabolic process aromatic compound catabolic process negative regulation of cellular biosynthetic process cellular nitrogen compound catabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process heterocycle catabolic process catabolic process macromolecule catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process histone mRNA catabolic process nuclear-transcribed mRNA catabolic process organic cyclic compound catabolic process nuclear histone mRNA catabolic process negative regulation of biosynthetic process organic substance 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 cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule cytosol protein-containing complex ribonucleoprotein complex intracellular anatomical structure cytoplasmic ribonucleoprotein granule cellular anatomical entity ribonucleoprotein granule intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm supramolecular complex non-membrane-bounded organelle cytoplasmic stress granule cytosol protein-containing complex ribonucleoprotein complex chromosome chromosome, telomeric region chromosomal region membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C, D	5'-R(APUPAPUPUPUP*UP)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, 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 National Science Foundation (DBI-1832184), 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 R01GM133198.