2P1B

Crystal structure of human nucleophosmin-core

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	d2p1bb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d2p1bh_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d2p1bi_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2p1ba_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2p1bc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2p1bd_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d2p1be_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d2p1bf_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d2p1bg_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d2p1bj_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Nucleoplasmin-like core domain	Nucleoplasmin-like core domain	automated matches	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	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
A	SCOP2 Family	Nucleoplasmin-like core domain	8072506	4003012	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	3002011	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Nucleoplasmin-like core domain	8072507	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	Nucleoplasmin	e2p1bB1	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	Nucleoplasmin	e2p1bH1	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)
I	Nucleoplasmin	e2p1bI1	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	e2p1bA1	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	e2p1bC1	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	e2p1bD1	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	e2p1bE1	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	Nucleoplasmin	e2p1bF1	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	Nucleoplasmin	e2p1bG1	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	Nucleoplasmin	e2p1bJ1	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)
B	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)
I	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)
C	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)
E	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)
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)

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 transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding RNA binding organic cyclic compound binding rRNA binding nucleic acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding protein binding binding histone binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding RNA binding organic cyclic compound binding rRNA binding nucleic acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding core promoter sequence-specific DNA binding transcription regulatory region nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosomal large subunit binding ribosome binding enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity kinase inhibitor activity kinase regulator activity chromatin binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity transcription coactivator activity transcription regulator activity transcription coregulator activity Tat protein binding unfolded protein binding identical protein binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding ribosomal small subunit binding	regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of cellular process negative regulation of biological process regulation of mRNA splicing, via spliceosome mRNA processing negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of mRNA splicing, via spliceosome organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process RNA processing negative regulation of mRNA processing regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process negative regulation of mRNA metabolic process organic substance metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of mRNA processing RNA splicing biological regulation regulation of macromolecule metabolic process gene expression regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of RNA splicing RNA splicing, via transesterification reactions negative regulation of biosynthetic process mRNA splicing, via spliceosome cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process regulation of catalytic activity negative regulation of catalytic activity regulation of transferase activity negative regulation of kinase activity negative regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process phosphorus metabolic process protein modification process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process regulation of molecular function regulation of kinase activity negative regulation of protein phosphorylation macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process protein metabolic process organonitrogen compound metabolic process negative regulation of protein kinase activity by regulation of protein phosphorylation negative regulation of molecular function negative regulation of protein kinase activity regulation of protein kinase activity negative regulation of phosphorus metabolic process regulation of phosphorylation negative regulation of phosphorylation cell cycle G2/M phase transition regulation of cell cycle phase transition regulation of cell cycle process positive regulation of biological process regulation of cell cycle G2/M phase transition cell cycle phase transition positive regulation of cell cycle G2/M phase transition positive regulation of cell cycle positive regulation of cell cycle phase transition positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process regulation of protein stability regulation of biological quality protein stabilization protein localization localization cellular localization cellular macromolecule localization macromolecule localization regulation of cellular component organization positive regulation of centrosome duplication microtubule cytoskeleton organization cellular component organization centrosome duplication centrosome cycle cellular component organization or biogenesis microtubule organizing center organization regulation of centrosome cycle regulation of microtubule-based process organelle organization regulation of centrosome duplication microtubule-based process cytoskeleton organization regulation of ribonuclease activity regulation of endoribonuclease activity regulation of hydrolase activity regulation of nuclease activity nucleocytoplasmic transport transport nuclear transport establishment of localization in cell intracellular transport establishment of localization regulation of growth growth regulation of cell growth cell growth cellular response to stimulus cellular response to stress response to stimulus response to stress cellular senescence regulation of localization regulation of protein localization positive regulation of protein localization to nucleolus positive regulation of protein localization to nucleus regulation of protein localization to nucleus protein localization to nucleus protein localization to nucleolus regulation of cellular localization protein localization to organelle positive regulation of protein localization regulation of protein localization to nucleolus positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of DNA-templated transcription DNA metabolic process DNA damage response DNA repair regulation of mRNA stability involved in cellular response to UV cellular response to environmental stimulus post-transcriptional regulation of gene expression cellular response to light stimulus RNA catabolic process mRNA catabolic process cellular response to radiation response to UV nucleobase-containing compound catabolic process nucleic acid catabolic process response to abiotic stimulus cellular response to abiotic stimulus response to light stimulus catabolic process macromolecule catabolic process regulation of mRNA catabolic process regulation of catabolic process organic cyclic compound catabolic process regulation of mRNA stability regulation of RNA stability response to radiation cellular response to UV organic substance catabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular response to nitrogen compound response to organic substance regulation of cellular response to stress organonitrogen compound biosynthetic process regulation of translational initiation by eIF2 alpha phosphorylation translational initiation response to organic cyclic compound cellular response to dsRNA regulation of translational initiation cellular response to organic cyclic compound response to nitrogen compound regulation of response to stimulus response to chemical regulation of translation in response to stress regulation of response to stress cellular response to organic substance regulation of eIF2 alpha phosphorylation by dsRNA response to dsRNA translation cellular response to chemical stimulus regulation of translation regulation of translational initiation in response to stress non-membrane-bounded organelle assembly cellular component biogenesis cellular component assembly regulation of centriole replication centriole replication centriole assembly organelle assembly regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus protein-containing complex localization ribosome biogenesis ribosomal small subunit export from nucleus organelle localization nuclear export ribosome localization negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of endodeoxyribonuclease activity regulation of deoxyribonuclease activity regulation of DNA metabolic process regulation of cellular component size homeostatic process cell volume homeostasis cellular homeostasis regulation of cell size regulation of anatomical structure size positive regulation of protein metabolic process regulation of protein ubiquitination positive regulation of post-translational protein modification positive regulation of protein modification process protein ubiquitination regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of post-translational protein modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal ribosomal large subunit export from nucleus signaling regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator regulation of signaling signal transduction by p53 class mediator regulation of cell communication signal transduction in response to DNA damage protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization chromatin organization protein-containing complex assembly chromatin remodeling nucleosome assembly nucleosome organization cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of translation positive regulation of gene expression establishment of protein localization nitrogen compound transport organic substance transport protein transport intracellular protein transport ribosomal large subunit biogenesis negative regulation of cell population proliferation regulation of cytoskeleton organization negative regulation of cell cycle negative regulation of centrosome cycle negative regulation of centrosome duplication negative regulation of cellular component organization negative regulation of cytoskeleton organization negative regulation of cell cycle process negative regulation of organelle organization ribosomal small subunit biogenesis ribosome assembly	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasm cytosol protein-containing complex small ribosomal subunit ribosomal subunit ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle large ribosomal subunit anchoring junction cell junction focal adhesion cell-substrate junction nucleolus granular component centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton spindle pole centrosome spindle spindle pole protein-DNA complex

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	IPR036824	Nucleoplasmin core domain superfamily	Homologous Superfamily
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Pharos: P06748	acute myeloid leukemia acute promyelocytic leukemia cancer lung adenocarcinoma lymphomatoid papulosis lung cancer lymphoplasmacytic lymphoma malignant glioma MALT lymphoma myopathy oligodendroglioma plasma cell myeloma psoriasis congenital anemia Disease Models, Animal acute myeloid leukemia acute promyelocytic leukemia cancer lung adenocarcinoma lymphomatoid papulosis lung cancer lymphoplasmacytic lymphoma malignant glioma MALT lymphoma myopathy oligodendroglioma plasma cell myeloma psoriasis congenital anemia Disease Models, Animal glioblastoma large cell medulloblastoma lymphatic system disease malignant colon neoplasm medulloblastoma non-Hodgkin lymphoma osteoarthritis primary cutaneous anaplastic large cell lymphoma chronic obstructive pulmonary disease subependymal giant cell astrocytoma gastric cancer hematologic disease malignant ependymoma malignant pancreatic neoplasm myeloid leukemia non-small cell lung carcinoma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor primitive neuroectodermal tumor diabetes mellitus gastric neoplasm hereditary diffuse gastric adenocarcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.