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- PDB-4n8m: Structural polymorphism in the N-terminal oligomerization domain ... -

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Basic information

Entry
Database: PDB / ID: 4n8m
TitleStructural polymorphism in the N-terminal oligomerization domain of NPM1
ComponentsNucleophosmin
KeywordsCHAPERONE / histone chaperone / nucleolar protein / phosphoprotein / structural polymorphism / pentamer / ribosome biogenesis / regulated unfolding
Function / homology
Function and homology information


TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / 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 / DNA-binding transcription factor binding => GO:0140297 / regulation of endodeoxyribonuclease activity ...TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / 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 / DNA-binding transcription factor binding => GO:0140297 / regulation of endodeoxyribonuclease activity / positive regulation of cell cycle G2/M phase transition / positive regulation of centrosome duplication / Deposition of new CENPA-containing nucleosomes at the centromere / SUMOylation of transcription cofactors / regulation of centriole replication / granular component / positive regulation of protein localization to nucleolus / positive regulation of cellular biosynthetic process / negative regulation of protein kinase activity by regulation of protein phosphorylation / protein kinase B binding / : / Tat protein binding / regulation of centrosome duplication / positive regulation of DNA metabolic process / positive regulation of DNA-directed DNA polymerase activity / cellular response to testosterone stimulus / spindle pole centrosome / cardiac muscle hypertrophy / cell volume homeostasis / centrosome cycle / nucleocytoplasmic transport / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of cardiac muscle cell apoptotic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-transcriptional regulation of gene expression / positive regulation of catalytic activity / protein kinase inhibitor activity / ribosomal large subunit binding / phosphatidylinositol-3,4,5-trisphosphate binding / negative regulation of mRNA splicing, via spliceosome / rRNA transcription / transcription factor binding / ribosomal small subunit binding / NF-kappaB binding / ribosomal large subunit export from nucleus / positive regulation of protein kinase activity / ribosomal small subunit export from nucleus / regulation of neuron apoptotic process / core promoter sequence-specific DNA binding / positive regulation of DNA replication / ribosomal large subunit biogenesis / positive regulation of protein ubiquitination / positive regulation of translation / liver regeneration / regulation of cell growth / protein-DNA complex / regulation of protein stability / protein localization / nuclear matrix / large ribosomal subunit / negative regulation of epithelial cell proliferation / cellular response to UV / unfolded protein binding / nucleosome assembly / p53 binding / positive regulation of NF-kappaB transcription factor activity / ribosomal small subunit biogenesis / small ribosomal subunit / histone binding / cellular response to hypoxia / negative regulation of neuron apoptotic process / transcription coactivator activity / protein stabilization / rRNA binding / regulation of cell cycle / nuclear speck / chromatin remodeling / ribonucleoprotein complex / negative regulation of cell population proliferation / negative regulation of gene expression / DNA repair / centrosome / chromatin binding / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Nucleoplasmin core domain / Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsMitrea, D. / Royappa, G. / Buljan, M. / Yun, M. / Pytel, N. / Satumba, J. / Nourse, A. / Park, C. / Babu, M.M. / White, S.W. / Kriwacki, R.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural polymorphism in the N-terminal oligomerization domain of NPM1.
Authors: Mitrea, D.M. / Grace, C.R. / Buljan, M. / Yun, M.K. / Pytel, N.J. / Satumba, J. / Nourse, A. / Park, C.G. / Madan Babu, M. / White, S.W. / Kriwacki, R.W.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,37110
Polymers73,0765
Non-polymers2955
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-63 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.675, 69.794, 88.630
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14615.280 Da / Num. of mol.: 5 / Fragment: N-TERMINAL DOMAIN OF NPM1, UNP residues 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npm1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q61937
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 0.6M 1,6 hexandiol, 10mM cobalt chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2009 / Details: Rosenbaum-Rock double-crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 49059 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.068 / Net I/σ(I): 23.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Num. unique all: 4192 / Rsym value: 0.317 / % possible all: 83.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1B

2p1b


Resolution: 1.802→37.26 Å / SU ML: 0.19 / σ(F): 1.33 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2493 5.09 %RANDOM
Rwork0.1632 ---
obs0.1646 49014 97.16 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.164 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.451 Å2-0 Å20.5786 Å2
2---4.8604 Å20 Å2
3----0.5906 Å2
Refinement stepCycle: LAST / Resolution: 1.802→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 5 227 4242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084118
X-RAY DIFFRACTIONf_angle_d1.265592
X-RAY DIFFRACTIONf_dihedral_angle_d12.6121516
X-RAY DIFFRACTIONf_chiral_restr0.091649
X-RAY DIFFRACTIONf_plane_restr0.006723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.802-1.83620.34161040.24962121X-RAY DIFFRACTION80
1.8362-1.87370.29561330.23252251X-RAY DIFFRACTION87
1.8737-1.91450.26171360.19992496X-RAY DIFFRACTION93
1.9145-1.9590.21961600.1782566X-RAY DIFFRACTION98
1.959-2.0080.20831380.15072618X-RAY DIFFRACTION99
2.008-2.06230.16861250.15112652X-RAY DIFFRACTION100
2.0623-2.12290.19591250.14932675X-RAY DIFFRACTION100
2.1229-2.19150.18931380.15822653X-RAY DIFFRACTION100
2.1915-2.26980.19661360.15692652X-RAY DIFFRACTION100
2.2698-2.36060.18161470.15732620X-RAY DIFFRACTION100
2.3606-2.46810.21361380.16952677X-RAY DIFFRACTION100
2.4681-2.59810.20551500.16992670X-RAY DIFFRACTION100
2.5981-2.76090.19681440.16992626X-RAY DIFFRACTION100
2.7609-2.9740.20191460.1642637X-RAY DIFFRACTION99
2.974-3.27310.17821190.15472666X-RAY DIFFRACTION99
3.2731-3.74630.16191570.15522627X-RAY DIFFRACTION99
3.7463-4.71850.15511480.13652649X-RAY DIFFRACTION98
4.7185-37.2680.19291490.18362665X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1741-0.1968-0.05010.40320.26280.7640.0258-0.14810.07560.1086-0.09470.29970.0734-0.15090.02910.1089-0.00060.02720.1366-0.01730.1659-36.9754-3.7397-22.1218
20.8967-0.04510.18290.6948-0.10070.74810.03720.15720.041-0.1374-0.00390.00880.0545-0.0192-0.01270.0945-0.0015-0.0060.10520.00690.0938-25.2826-5.8264-38.0974
30.73040.06870.13180.5192-0.10310.9115-0.00780.1336-0.09090.0169-0.0239-0.17310.01420.19030.00380.09360.0222-0.00050.1291-0.02930.1553-6.7208-6.2228-32.239
41.31640.02990.01460.29170.41550.7843-0.016-0.2205-0.06310.27080.0188-0.12830.1270.1116-0.01170.19120.0442-0.04070.1664-0.01960.1364-6.5325-4.4062-12.4725
50.92120.25030.11980.52510.13450.35470.0763-0.59280.14220.3907-0.13230.13180.2633-0.1551-0.0060.2762-0.02310.05950.2634-0.02470.0553-25.4288-3.2219-6.1772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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