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- PDB-4iry: Influenza A virus tail-loop free nucleoprotein at 2.8 A resolution -

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Basic information

Entry
Database: PDB / ID: 4iry
TitleInfluenza A virus tail-loop free nucleoprotein at 2.8 A resolution
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / Nucleoprotein / Oligomerization / RNA binding / RNP assembly / RNA / nucleus
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYe, Q. / Mata, D.A. / Tao, Y.J.
CitationJournal: MBio / Year: 2012
Title: Biochemical and structural evidence in support of a coherent model for the formation of the double-helical influenza a virus ribonucleoprotein.
Authors: Ye, Q. / Guu, T.S. / Mata, D.A. / Kuo, R.L. / Smith, B. / Krug, R.M. / Tao, Y.J.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Refinement description
Revision 1.2Aug 2, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
B: Nucleocapsid protein
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)109,4952
Polymers109,4952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-11 kcal/mol
Surface area38550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.183, 155.618, 97.774
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleocapsid protein


Mass: 54747.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Wilson-Smith/1933(H1N1) / Gene: NP, nucleoprotein / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) Singles / References: UniProt: Q1K9H2

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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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris pH8.5, 18% PEG3350, 10% Glycerol, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 21821 / Num. obs: 21286 / % possible obs: 97.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.5 / Num. unique all: 878 / % possible all: 79

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IQH

2iqh


Resolution: 2.8→50 Å
RfactorNum. reflection% reflection
Rfree0.2978 2109 -
Rwork0.2415 --
all-22150 -
obs-21281 96.1 %
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 0 0 6586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.8→2.82 Å
RfactorNum. reflection% reflection
Rfree0.2978 19172 -
Rwork0.2415 --
obs-21281 96.1 %

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