3MD1

Crystal Structure of the Second RRM Domain of Yeast Poly(U)-Binding Protein (Pub1)

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)
A	d3md1a1	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d3md1a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3md1b_	Alpha and beta proteins (a+b)	Ferredoxin-like	RNA-binding domain, RBD, aka RNA recognition motif (RRM)	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	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	8061933	3000110	SCOP2B (2022-06-29)
B	SCOP2 Family	Canonical RBD	8061932	4000236	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	RNA-binding domain, RBD	8061933	3000110	SCOP2 (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	RRM_1	e3md1A1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)
B	RRM_1	e3md1B1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) 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	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	Nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1	RNA binding binding nucleic acid binding mRNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding poly-pyrimidine tract binding poly(U) RNA binding single-stranded RNA binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process negative regulation of cellular process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of mRNA stability regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of RNA stability nucleic acid catabolic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of mRNA metabolic process regulation of metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress response to starvation cellular response to glucose starvation cellular response to starvation cellular component biogenesis cellular component organization organelle organization cellular component assembly stress granule assembly organelle assembly membraneless organelle assembly cellular component organization or biogenesis cellular component disassembly protein-containing complex organization protein-containing complex disassembly translation translational termination protein metabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process	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 P-body membrane-bounded organelle nucleus 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 P-body membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000504	RNA recognition motif domain	Domain
A, B	IPR003954	RNA recognition motif domain, eukaryotes	Domain
A, B	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B	IPR052462	SRA stem-loop-interacting RNA-binding protein/Glycine-rich RNA-binding-like	Family
A, B	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

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.