6A6J | pdb_00006a6j

Crystal structure of Zebra fish Y-box protein1 (YB-1) Cold-shock domain in complex with 6mer m5C RNA

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)
C	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	V-set	e6a6jA1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: HTH	T: Ribbon-helix-helix	F: V-set	ECOD (v294.1)
C	TetR_N	e6a6jC1	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: TetR_N	ECOD (v294.1)

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 (utative)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, D	RNA (5'-R(PCPAPUP(5MC)P*U)-3')	-	-	-
A, C	Zebra fish Y-box protein1 (YB-1)	binding nucleic acid binding DNA binding RNA binding mRNA 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 double-stranded DNA binding chromatin binding regulatory RNA binding binding nucleic acid binding DNA binding RNA binding mRNA 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 double-stranded DNA binding chromatin binding regulatory RNA binding miRNA binding protein binding enzyme binding GTPase 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 nucleobase-containing compound biosynthetic process mRNA processing RNA biosynthetic process nucleic acid biosynthetic process RNA processing positive regulation of cell division cell division regulation of cell division developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis embryonic morphogenesis anatomical structure development embryo development embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development RNA splicing DNA-templated transcription regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of developmental process cellular developmental process negative regulation of developmental process negative regulation of striated muscle cell differentiation negative regulation of muscle cell differentiation regulation of cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation muscle structure development regulation of muscle cell differentiation cell differentiation negative regulation of cell differentiation striated muscle cell differentiation localization protein localization to cytoplasmic stress granule protein localization to organelle macromolecule localization intracellular protein localization negative regulation of RNA biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic 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 epidermis development tissue development RNA transport nitrogen compound transport transport nucleic acid transport establishment of localization tRNA transport establishment of RNA localization RNA localization nucleobase-containing compound transport negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of mRNA 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 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 response to peptide response to interleukin-7 response to chemical response to cytokine cellular response to cytokine stimulus cellular response to interleukin-7	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol protein-containing complex nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex ribonucleoprotein complex U12-type spliceosomal complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule histone pre-mRNA 3'end processing complex cell periphery plasma membrane membrane membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen synapse cell junction CRD-mediated mRNA stability complex intracellular protein-containing complex P-body endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

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

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.

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