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- PDB-5tjw: Influenza A virus Nucleoprotein in Complex with Inhibitory Nanobody -

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Basic information

Entry
Database: PDB / ID: 5tjw
TitleInfluenza A virus Nucleoprotein in Complex with Inhibitory Nanobody
Components
  • NP-specific inhibitory VHH
  • Nucleoprotein
KeywordsViral Protein/Immune System / Influenza / nucleoprotein / VHH / inhibitory / Viral Protein-Immune System complex
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.231 Å
AuthorsHanke, L. / Knockenhauer, K.E. / Ploegh, H.L. / Schwartz, T.U.
CitationJournal: MBio / Year: 2016
Title: The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment.
Authors: Hanke, L. / Knockenhauer, K.E. / Brewer, R.C. / van Diest, E. / Schmidt, F.I. / Schwartz, T.U. / Ploegh, H.L.
History
DepositionOct 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
K: NP-specific inhibitory VHH


Theoretical massNumber of molelcules
Total (without water)72,5172
Polymers72,5172
Non-polymers00
Water00
1
A: Nucleoprotein
K: NP-specific inhibitory VHH

A: Nucleoprotein
K: NP-specific inhibitory VHH

A: Nucleoprotein
K: NP-specific inhibitory VHH


Theoretical massNumber of molelcules
Total (without water)217,5526
Polymers217,5526
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Unit cell
Length a, b, c (Å)137.548, 137.548, 137.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsHexamer confirmed by gel filtration

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Components

#1: Protein Nucleoprotein


Mass: 57583.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/WSN/1933(H1N1)) / Strain: A/WSN/1933(H1N1) / Gene: NP / Plasmid: pet30b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B4URF1, UniProt: Q1K9H2*PLUS
#2: Antibody NP-specific inhibitory VHH


Mass: 14934.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pHEN-6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
Has protein modificationY

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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: 2.99 Å3/Da / Density % sol: 58.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, 1.5 M ammonium sulfate, 0.025% (v/v) dichloromethane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.22→97.26 Å / Num. obs: 14189 / % possible obs: 99 % / Redundancy: 9.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.178 / Net I/σ(I): 15.4
Reflection shellResolution: 3.22→3.34 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.687 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IQH, 4KRL

2iqh

4krl


Resolution: 3.231→97.261 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1419 10 %
Rwork0.2044 --
obs0.2101 14188 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.231→97.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 0 0 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054686
X-RAY DIFFRACTIONf_angle_d0.6336312
X-RAY DIFFRACTIONf_dihedral_angle_d9.1922841
X-RAY DIFFRACTIONf_chiral_restr0.047678
X-RAY DIFFRACTIONf_plane_restr0.003833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2313-3.34680.35341450.27161265X-RAY DIFFRACTION100
3.3468-3.48080.33461420.24691252X-RAY DIFFRACTION100
3.4808-3.63920.291360.23651256X-RAY DIFFRACTION100
3.6392-3.83110.27971410.22251261X-RAY DIFFRACTION100
3.8311-4.07110.26471410.19941265X-RAY DIFFRACTION100
4.0711-4.38540.23431420.18711280X-RAY DIFFRACTION100
4.3854-4.82680.20921350.17411255X-RAY DIFFRACTION100
4.8268-5.52510.25251430.18971299X-RAY DIFFRACTION100
5.5251-6.96080.29121440.22791281X-RAY DIFFRACTION100
6.9608-97.30520.23771500.18621355X-RAY DIFFRACTION100

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