7F3J | pdb_00007f3j

Crystal structure of human YBX2 CSD in complex with m5C RNA in space group P1

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	Peptidase_S29	e7f3jG1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_S29	ECOD (v294.1)
E	Peptidase_S29	e7f3jE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_S29	ECOD (v294.1)
C	Peptidase_S29	e7f3jC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_S29	ECOD (v294.1)
A	Peptidase_S29	e7f3jA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_S29	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (utative)
E	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, E, G	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, F, H	RNA (5'-R(UPCPAPUP*(5MC))-3')	-	-	-
A, C, E, G	Y-box-binding protein 2	DNA binding binding nucleic acid binding RNA binding	multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process developmental process multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process regulation of multicellular organismal process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of biosynthetic process regulation of cellular process regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process cellular developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation oocyte development cell differentiation anatomical structure development germ cell development oocyte differentiation protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression translational attenuation protein metabolic process regulation of protein metabolic process translation regulation of translation	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: Q9Y2T7	cutaneous lupus erythematosus osteosarcoma vascular disease Hashimoto thyroiditis psoriasis hypothyroidism ulcerative colitis

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.