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- PDB-2iqh: Influenza A virus nucleoprotein NP at 3.2A resolution -

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Basic information

Entry
Database: PDB / ID: 2iqh
TitleInfluenza A virus nucleoprotein NP at 3.2A resolution
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / oligomerization / RNA binding / NLS / polymerase binding
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
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 3.2 Å
AuthorsYe, Q. / Tao, Y.J.
CitationJournal: Nature / Year: 2006
Title: The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA.
Authors: Ye, Q. / Krug, R.M. / Tao, Y.J.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Nucleocapsid protein
B: Nucleocapsid protein
C: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)170,4183
Polymers170,4183
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-41 kcal/mol
Surface area56620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.099, 135.105, 195.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nucleocapsid protein


Mass: 56806.047 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Wilson-Smith/1933(H1N1))
Genus: Influenzavirus A / Species: Influenza A virus / Strain: A/Wilson-Smith/1933(H1N1) / Gene: NP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM 2(DE3) SinglesTM / References: UniProt: Q1I2B5, UniProt: Q1K9H2*PLUS

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris HCl, 3% PEG 8000, 10% Glycerol, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9792
SYNCHROTRONCHESS F221.0397, 1.0064, 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.03971
31.00641
ReflectionResolution: 3.2→30 Å / Num. obs: 26880 / % possible obs: 99.3 % / Observed criterion σ(I): 13.2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.843 / SU B: 30.278 / SU ML: 0.524 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.653 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31814 1297 4.8 %RANDOM
Rwork0.27112 ---
obs0.27341 25500 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 74.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å20 Å2
2---0.11 Å20 Å2
3---1.63 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10162 0 0 0 10162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210303
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.95513850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.59851270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77322.057491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.305151864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.87915137
X-RAY DIFFRACTIONr_chiral_restr0.0970.21508
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027790
X-RAY DIFFRACTIONr_nbd_refined0.2970.25927
X-RAY DIFFRACTIONr_nbtor_refined0.3360.27206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2454
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.210
X-RAY DIFFRACTIONr_mcbond_it1.4461.56486
X-RAY DIFFRACTIONr_mcangle_it2.456210214
X-RAY DIFFRACTIONr_scbond_it3.01934190
X-RAY DIFFRACTIONr_scangle_it4.7944.53636
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 84 -
Rwork0.261 1832 -
obs-1916 100 %

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