2VTX | pdb_00002vtx

ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY

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)
I [auth J]	d2vtxj_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
J [auth K]	d2vtxk_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
H [auth I]	d2vtxi_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
G [auth H]	d2vtxh_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
F [auth G]	d2vtxg_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
E	d2vtxe_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
D	d2vtxd_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
C	d2vtxc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
B	d2vtxb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	AFRICAN CLAWED FROG (Xenopus laevis ) [TaxId: 8355 ],	SCOPe (2.08)
A	d2vtxa_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	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)
I [auth J]	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
J [auth K]	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
G [auth H]	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	3002011	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoplasmin-like core domain	8037830	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)
I [auth J]	Nucleoplasmin	e2vtxJ1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
J [auth K]	Nucleoplasmin	e2vtxK1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
H [auth I]	Nucleoplasmin	e2vtxI1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
G [auth H]	Nucleoplasmin	e2vtxH1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
F [auth G]	Nucleoplasmin	e2vtxG1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
E	Nucleoplasmin	e2vtxE1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
D	Nucleoplasmin	e2vtxD1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
C	Nucleoplasmin	e2vtxC1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
B	Nucleoplasmin	e2vtxB1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)
A	Nucleoplasmin	e2vtxA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Nucleoplasmin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth J]	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
J [auth K]	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
H [auth I]	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
G [auth H]	2.60.120.340	Mainly Beta	Sandwich	Jelly Rolls	Nucleoplasmin core domain	CATH (4.3.0)
F [auth G]	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)
B	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
I [auth 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
A, B, C, D, E, A, B, C, D, E, F [auth G], G [auth H], H [auth I], J [auth K]	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
I [auth J]	NPM-A PROTEIN	protein binding binding histone binding chromatin binding importin-alpha family protein binding RNA binding nucleic acid binding protein carrier chaperone histone chaperone activity molecular carrier activity protein-containing complex binding nucleosome binding	regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication positive regulation of DNA metabolic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication organelle assembly sexual reproduction reproductive process fertilization sperm DNA decondensation cellular component organization cellular component biogenesis male pronucleus assembly organelle organization nucleus organization cellular component assembly chromatin organization cellular component organization or biogenesis single fertilization 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 cytoplasm nucleoplasm
A, B, C, D, E, A, B, C, D, E, F [auth G], G [auth H], H [auth I], J [auth K]	NPM-A PROTEIN	protein binding binding histone binding chromatin binding importin-alpha family protein binding RNA binding nucleic acid binding protein carrier chaperone histone chaperone activity molecular carrier activity protein-containing complex binding nucleosome binding	regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process regulation of cellular process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process DNA replication positive regulation of DNA metabolic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication organelle assembly sexual reproduction reproductive process fertilization sperm DNA decondensation cellular component organization cellular component biogenesis male pronucleus assembly organelle organization nucleus organization cellular component assembly chromatin organization cellular component organization or biogenesis single fertilization 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 cytoplasm nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth J]	IPR004301	Nucleoplasmin family	Family
I [auth J]	IPR024057	Nucleoplasmin core domain	Domain
I [auth J]	IPR036824	Nucleoplasmin core domain superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F [auth G], G [auth H], H [auth I], J [auth K]	IPR004301	Nucleoplasmin family	Family
A, B, C, D, E, A, B, C, D, E, F [auth G], G [auth H], H [auth I], J [auth K]	IPR024057	Nucleoplasmin core domain	Domain
A, B, C, D, E, A, B, C, D, E, F [auth G], G [auth H], H [auth I], J [auth K]	IPR036824	Nucleoplasmin core domain superfamily	Homologous Superfamily

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.