1DTJ

CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1dtjb_	Alpha and beta proteins (a+b)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Neuro-oncological ventral antigen 2, nova-2, KH3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1dtjc_	Alpha and beta proteins (a+b)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Neuro-oncological ventral antigen 2, nova-2, KH3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1dtjd_	Alpha and beta proteins (a+b)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Neuro-oncological ventral antigen 2, nova-2, KH3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1dtja_	Alpha and beta proteins (a+b)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Neuro-oncological ventral antigen 2, nova-2, KH3	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)
B	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8035101	3001023	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8035101	3001023	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8035101	3001023	SCOP2B (2022-06-29)
A	SCOP2 Family	Eukaryotic type KH-domain (KH-domain type I)	8022721	4001190	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8035101	3001023	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)
B	KH_1_1	e1dtjB1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_1	ECOD (1.6)
C	KH_1_1	e1dtjC1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_1	ECOD (1.6)
D	KH_1_1	e1dtjD1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_1	ECOD (1.6)
A	KH_1_1	e1dtjA1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
D	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
A	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00013	KH domain (KH_1)	KH domain	KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RNA-BINDING NEUROONCOLOGICAL VENTRAL ANTIGEN 2	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding sequence-specific mRNA binding	developmental process multicellular organismal process cellular developmental process central nervous system neuron development cell development nervous system development generation of neurons central nervous system neuron differentiation multicellular organism development neurogenesis central nervous system development neuron differentiation cell differentiation neuron development anatomical structure development developmental process multicellular organismal process cellular developmental process central nervous system neuron development cell development nervous system development generation of neurons central nervous system neuron differentiation multicellular organism development neurogenesis central nervous system development neuron differentiation cell differentiation neuron development anatomical structure development cellular process system development regulation of biological process regulation of cellular process biological regulation RNA metabolic process primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process metabolic process regulation of nucleobase-containing compound metabolic process macromolecule metabolic process regulation of metabolic process axonogenesis response to stimulus cell projection organization neuron projection development cell projection morphogenesis neuron projection morphogenesis taxis regulation of axon guidance chemotaxis regulation of cell projection organization response to external stimulus regulation of response to stimulus response to chemical regulation of locomotion regulation of neuron projection development regulation of cellular component organization regulation of response to external stimulus plasma membrane bounded cell projection morphogenesis cell morphogenesis cellular component organization cellular component organization or biogenesis locomotion plasma membrane bounded cell projection organization axon guidance axon development regulation of chemotaxis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection guidance regulation of plasma membrane bounded cell projection organization RNA splicing gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing alternative mRNA splicing, via spliceosome regulation of mRNA splicing, via spliceosome regulation of biosynthetic process regulation of mRNA processing regulation of RNA splicing regulation of gene expression regulation of alternative mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process regulation of mRNA metabolic process negative regulation of cold-induced thermogenesis homeostatic process negative regulation of metabolic process negative regulation of biological process adaptive thermogenesis multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis negative regulation of cellular process temperature homeostasis regulation of multicellular organismal process negative regulation of multicellular organismal process	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, B, C, D	IPR047274	RNA-binding protein Nova-1/2, type I K Homology domain 3	Domain
A, B, C, D	IPR047275	RNA-binding protein Nova-1/2, type I K Homology domain 1	Domain
A, B, C, D	IPR004087	K Homology domain	Domain
A, B, C, D	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A, B, C, D	IPR004088	K Homology domain, type 1	Domain
A, B, C, D	IPR047276	RNA-binding protein Nova-1/2, type I K Homology domain 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9UNW9	atypical teratoid rhabdoid tumor heart disease malignant ependymoma pilocytic astrocytoma gallbladder disease invasive ductal breast carcinoma malignant glioma progressive supranuclear palsy glioblastoma large cell medulloblastoma medulloblastoma

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.