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- PDB-3tj0: Crystal Structure of Influenza B Virus Nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 3tj0
TitleCrystal Structure of Influenza B Virus Nucleoprotein
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / RNA-binding / Homo-oligomerization / Transcription regulation / Nucleus
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.233 Å
AuthorsNg, A.K.L. / Zhang, H. / Liu, J. / Au, S.W.N. / Wang, J. / Shaw, P.C.
CitationJournal: J.Virol. / Year: 2012
Title: Structural basis for RNA binding and homo-oligomer formation by influenza B virus nucleoprotein
Authors: Ng, A.K.L. / Lam, M.K.H. / Zhang, H. / Liu, J. / Au, S.W.N. / Chan, P.K.S. / Wang, J. / Shaw, P.C.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)123,7642
Polymers123,7642
Non-polymers00
Water0
1
A: Nucleoprotein

A: Nucleoprotein

B: Nucleoprotein

B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)247,5294
Polymers247,5294
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area46420 Å2
2
B: Nucleoprotein

B: Nucleoprotein

A: Nucleoprotein

A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)247,5294
Polymers247,5294
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_555x+1/2,-y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)106.951, 123.342, 198.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Nucleoprotein /


Mass: 61882.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Managua/4577.01/2008 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: C4LQ26
Sequence detailsTHIS SEQUENCE IS THE NATURAL POLYMORPHISM OF THE PROTEIN.

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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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.4M sodium-potassium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 21367 / Num. obs: 19883 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1998 / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
Cootmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q06

2q06


Resolution: 3.233→47.055 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 31.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2914 1023 5.15 %Random
Rwork0.245 ---
obs0.2474 19862 92.98 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.073 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.303 Å20 Å2-0 Å2
2--54.1203 Å20 Å2
3----34.8173 Å2
Refinement stepCycle: LAST / Resolution: 3.233→47.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7022 0 0 0 7022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027128
X-RAY DIFFRACTIONf_angle_d0.7299563
X-RAY DIFFRACTIONf_dihedral_angle_d11.9432724
X-RAY DIFFRACTIONf_chiral_restr0.0481075
X-RAY DIFFRACTIONf_plane_restr0.0021228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2326-3.4030.40131540.3393266594
3.403-3.61610.35421530.3012268494
3.6161-3.89520.31691580.25270194
3.8952-4.28690.27091470.2123268994
4.2869-4.90670.2751310.1954268793
4.9067-6.17970.29121420.2531267092
6.1797-47.05970.23541380.2353274390

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