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- PDB-2vxd: The structure of the C-terminal domain of Nucleophosmin -

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Basic information

Entry
Database: PDB / ID: 2vxd
TitleThe structure of the C-terminal domain of Nucleophosmin
ComponentsNUCLEOPHOSMINNPM1
KeywordsNUCLEAR PROTEIN / CHROMOSOMAL REARRANGEMENT / PROTO-ONCOGENE / PHOSPHOPROTEIN / ALTERNATIVE SPLICING / AML / NUCLEUS / NUCLEOLUS / RNA-BINDING / ACETYLATION
Function / homology
Function and homology information


regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / positive regulation of cell cycle G2/M phase transition / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of centrosome duplication / regulation of centriole replication ...regulation of mRNA stability involved in cellular response to UV / regulation of eIF2 alpha phosphorylation by dsRNA / positive regulation of cell cycle G2/M phase transition / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of centrosome duplication / regulation of centriole replication / positive regulation of protein localization to nucleolus / negative regulation of protein kinase activity by regulation of protein phosphorylation / regulation of centrosome duplication / Tat protein binding / cell volume homeostasis / nucleocytoplasmic transport / spindle pole centrosome / Nuclear import of Rev protein / centrosome cycle / rRNA export from nucleus / protein kinase inhibitor activity / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / regulation of DNA damage response, signal transduction by p53 class mediator / ribosomal large subunit binding / negative regulation of mRNA splicing, via spliceosome / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / ribosomal small subunit binding / Deposition of new CENPA-containing nucleosomes at the centromere / NF-kappaB binding / ribosomal large subunit biogenesis / ribosomal small subunit biogenesis / cell aging / core promoter sequence-specific DNA binding / positive regulation of protein kinase activity / positive regulation of protein ubiquitination / ribosome assembly / SUMOylation of transcription cofactors / intracellular protein transport / protein localization / regulation of cell growth / positive regulation of translation / nucleosome assembly / protein-DNA complex / cellular response to UV / DNA-binding transcription factor binding / large ribosomal subunit / unfolded protein binding / ribonucleoprotein complex / small ribosomal subunit / histone binding / protein N-terminus binding / chromatin remodeling / protein stabilization / rRNA binding / transcription coactivator activity / positive regulation of NF-kappaB transcription factor activity / nuclear speck / centrosome / negative regulation of cell population proliferation / DNA repair / focal adhesion / chromatin binding / nucleolus / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / positive regulation of transcription, DNA-templated / signal transduction / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / RNA binding / membrane / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nucleophosmin, C-terminal domain / Nucleophosmin C-terminal domain / Nucleophosmin, C-terminal / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR
AuthorsBycroft, M. / Grummitt, C.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Consequences of Nucleophosmin Mutations in Acute Myeloid Leukemia.
Authors: Grummitt, C.G. / Townsley, F.M. / Johnson, C.M. / Warren, A.J. / Bycroft, M.
History
DepositionJul 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
Revision 1.2Jun 23, 2021Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOPHOSMIN


Theoretical massNumber of molelcules
Total (without water)6,1831
Polymers6,1831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein NUCLEOPHOSMIN / NPM1 / NPM / NUCLEOLAR PHOSPHOPROTEIN B23 / NUMATRIN / NUCLEOLAR PROTEIN NO38


Mass: 6183.121 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 214-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P06748
Sequence detailsTWO EXTRA GLYCINE RESIDUES AT THE N-TERMINUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionsIonic strength: 150 mM / pH: 6.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIBrukerAVANCE II7002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 150 / Conformers submitted total number: 20

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