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- PDB-2p1b: Crystal structure of human nucleophosmin-core -

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Basic information

Entry
Database: PDB / ID: 2p1b
TitleCrystal structure of human nucleophosmin-core
ComponentsNucleophosmin
KeywordsCHAPERONE / Decamer
Function / homology
Function and homology information


regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation ...regulation of eIF2 alpha phosphorylation by dsRNA / regulation of mRNA stability involved in cellular response to UV / regulation of endoribonuclease activity / negative regulation of centrosome duplication / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / regulation of centriole replication / granular component / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / negative regulation of protein kinase activity by regulation of protein phosphorylation / SARS-CoV-1-host interactions / Tat protein binding / regulation of centrosome duplication / ALK mutants bind TKIs / spindle pole centrosome / Nuclear import of Rev protein / centrosome cycle / nucleocytoplasmic transport / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / protein kinase inhibitor activity / ribosomal large subunit binding / ribosomal small subunit binding / NF-kappaB binding / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / Nuclear events stimulated by ALK signaling in cancer / ribosomal subunit export from nucleus / core promoter sequence-specific DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / ribosome assembly / SUMOylation of transcription cofactors / ribosomal large subunit biogenesis / positive regulation of translation / protein-DNA complex / intracellular protein transport / PKR-mediated signaling / protein localization / : / cellular response to UV / cellular senescence / Signaling by ALK fusions and activated point mutants / unfolded protein binding / nucleosome assembly / ribosomal small subunit biogenesis / positive regulation of NF-kappaB transcription factor activity / histone binding / DNA-binding transcription factor binding / transcription coactivator activity / rRNA binding / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation / DNA repair / focal adhesion / centrosome / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleoplasmin core domain / Nucleophosmin, C-terminal / Nucleophosmin C-terminal domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLee, H.H. / Kim, H.S. / Kang, J.Y. / Lee, B.I. / Ha, J.Y. / Yoon, H.J. / Lim, S.O. / Jung, G. / Suh, S.W.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of human nucleophosmin-core reveals plasticity of the pentamer-pentamer interface
Authors: Lee, H.H. / Kim, H.S. / Kang, J.Y. / Lee, B.I. / Ha, J.Y. / Yoon, H.J. / Lim, S.O. / Jung, G. / Suh, S.W.
History
DepositionMar 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleophosmin
B: Nucleophosmin
C: Nucleophosmin
D: Nucleophosmin
E: Nucleophosmin
F: Nucleophosmin
G: Nucleophosmin
H: Nucleophosmin
I: Nucleophosmin
J: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)135,44310
Polymers135,44310
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nucleophosmin
B: Nucleophosmin
C: Nucleophosmin
D: Nucleophosmin
E: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)67,7225
Polymers67,7225
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-64 kcal/mol
Surface area18930 Å2
MethodPISA, PQS
3
F: Nucleophosmin
G: Nucleophosmin
H: Nucleophosmin
I: Nucleophosmin
J: Nucleophosmin


Theoretical massNumber of molelcules
Total (without water)67,7225
Polymers67,7225
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-64 kcal/mol
Surface area18970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.262, 107.841, 108.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Nucleophosmin / NPM / Nucleolar phosphoprotein B23 / Numatrin / Nucleolar protein NO38


Mass: 13544.327 Da / Num. of mol.: 10 / Fragment: N-TERMINAL CORE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-21A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06748
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50MM AMMONIUM SULFATE, 50MM BIS-TRIS PH 6.5, 30%(W/V) PENTAERYTHRITOL ETHOXYLATE (15/4 EO/OH), pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2005 / Details: MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 31402 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.5 Å2
Reflection shellResolution: 2.75→2.85 Å / % possible all: 82.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XE0

1xe0


Resolution: 2.75→19.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 108133.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2915 10 %RANDOM
Rwork0.213 ---
obs0.213 29279 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.91 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20 Å20 Å2
2---8.11 Å20 Å2
3---3.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 0 86 7686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 448 10.3 %
Rwork0.331 3890 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM

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