1XB9 | pdb_00001xb9

The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus

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)
B	d1xb9b1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
B	d1xb9b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
G	d1xb9g1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
G	d1xb9g2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
J	d1xb9j1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
J	d1xb9j2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
I	d1xb9i1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
I	d1xb9i2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
H	d1xb9h1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
H	d1xb9h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
F	d1xb9f1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
F	d1xb9f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
E	d1xb9e1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
E	d1xb9e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
D	d1xb9d1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
D	d1xb9d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
C	d1xb9c1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
C	d1xb9c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
A	d1xb9a1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	Nucleophosmin (NO38)	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
A	d1xb9a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	African clawed frog (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoplasmin-like core domain	8043849	3002011	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)
B	Rhv	e1xb9B1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
G	Rhv	e1xb9G1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
J	Rhv	e1xb9J1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
I	Rhv	e1xb9I1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
H	Rhv	e1xb9H1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
F	Rhv	e1xb9F1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
E	Rhv	e1xb9E1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
D	Rhv	e1xb9D1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
C	Rhv	e1xb9C1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)
A	Rhv	e1xb9A1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Rhv	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
G	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
J	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
I	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
H	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
F	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
E	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
D	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
C	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
A	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF03066	Nucleoplasmin/nucleophosmin domain (Nucleoplasmin)	Nucleoplasmin/nucleophosmin domain	Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Nucleophosmin	protein binding binding histone binding chromatin binding RNA binding nucleic acid binding identical protein binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis establishment of organelle localization cellular localization nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis establishment of organelle localization cellular localization nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization localization ribosomal small subunit export from nucleus organelle localization establishment of localization in cell nuclear export ribosome localization cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair ribosomal small subunit biogenesis regulation of biological process microtubule organizing center organization regulation of cellular process regulation of cellular component organization regulation of centrosome cycle regulation of cell cycle process microtubule cytoskeleton organization biological regulation regulation of microtubule-based process cellular component organization centrosome duplication organelle organization centrosome cycle regulation of centrosome duplication microtubule-based process cell cycle regulation of cell cycle cytoskeleton organization cell cycle process ribosomal large subunit export from nucleus positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process chromatin organization chromatin remodeling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton protein-containing complex ribonucleoprotein complex cytoplasm nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR032569	Nucleophosmin, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR004301	Nucleoplasmin family	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR024057	Nucleoplasmin core domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036824	Nucleoplasmin core domain superfamily	Homologous Superfamily