Annotations: 5YTX

Crystal structure of YB1 cold-shock domain in complex with UCAACU

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8036377	3000135	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	Flavin containing amine oxidoreductase / NAD(P)-binding Rossmann-like domain	e5ytxA1	A: alpha arrays	X: PriB N-terminal domain-like	H: Ubiquitin-related	T: Ubiquitin-like	F: Flavin containing amine oxidoreductase / NAD(P)-binding Rossmann-like domain	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00313	'Cold-shock' DNA-binding domain (CSD)	'Cold-shock' DNA-binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	RNA (5'-R(PUPCPAPAPCPU)-3')	-	-	-
A	Nuclease-sensitive element-binding protein 1	binding nucleic acid binding chromatin binding RNA binding regulatory RNA binding miRNA binding protein binding enzyme binding GTPase binding DNA binding mRNA binding double-stranded DNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity binding nucleic acid binding chromatin binding RNA binding regulatory RNA binding miRNA binding protein binding enzyme binding GTPase binding DNA binding mRNA binding double-stranded DNA binding protein-RNA adaptor activity protein-macromolecule adaptor activity C5-methylcytidine-containing RNA reader activity molecular adaptor activity sequence-specific DNA binding sequence-specific double-stranded DNA binding single-stranded DNA binding	regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA stabilization regulation of cellular process negative regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA stabilization mRNA catabolic process regulation of biological process negative regulation of metabolic process primary metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process catabolic process positive regulation of biological process RNA metabolic process macromolecule catabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process positive regulation of biosynthetic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of catabolic process biological regulation negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of macromolecule metabolic process regulation of catabolic process gene expression mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of mRNA stability CRD-mediated mRNA stabilization RNA stabilization negative regulation of biosynthetic process positive regulation of gene expression regulation of RNA stability cellular process regulation of mRNA metabolic process protein biosynthetic process negative regulation of translation protein metabolic process negative regulation of protein metabolic process regulation of protein metabolic process translation regulation of translation developmental process epidermis development anatomical structure development tissue development animal gross anatomical part developmental process RNA transport nitrogen compound transport transport nucleic acid transport establishment of localization localization tRNA transport establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process mRNA processing RNA processing positive regulation of cell division cell division regulation of cell division multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis embryo development RNA splicing negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of mRNA metabolic process positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay mRNA destabilization regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay RNA destabilization nuclear-transcribed mRNA catabolic process positive regulation of catabolic process positive regulation of mRNA catabolic process miRNA transport regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of protein metabolic process positive regulation of translation positive regulation of cytoplasmic translation cytoplasmic translation regulation of cytoplasmic translation cellular response to stimulus response to stimulus regulation of cellular senescence cellular senescence negative regulation of cellular senescence cellular response to stress response to stress protein localization to cytoplasmic stress granule protein localization to organelle intracellular protein localization positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA biosynthetic 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 histone pre-mRNA 3'end processing complex membrane-bounded organelle protein-containing 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 histone pre-mRNA 3'end processing complex membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle ribonucleoprotein complex extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen synapse cell junction spliceosomal complex U12-type spliceosomal complex CRD-mediated mRNA stability complex intracellular protein-containing complex P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002059	Cold-shock protein Csp, DNA-binding	Domain
A	IPR019844	Cold-shock domain, conserved site	Conserved Site
A	IPR011129	Cold-shock domain	Domain
A	IPR050181	Cold shock domain-containing protein	Family
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: P67809	Neoplasm Recurrence, Local breast carcinoma malignant colon neoplasm benign colon neoplasm colonic neoplasm breast cancer

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.