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- PDB-8twp: Influenza A virus (A/Aichi/2/1968(H3N2) nucleoprotein mutant - 2-... -

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Basic information

Entry
Database: PDB / ID: 8twp
TitleInfluenza A virus (A/Aichi/2/1968(H3N2) nucleoprotein mutant - 2-7 deleted, R416A
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / nucleoprotein / influenza
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
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: 2.9 Å
AuthorsYoon, J. / Zhang, Y.M. / Grant, R.A. / Shoulders, M.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CAREER Award 1652390 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136354 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI168166 United States
CitationJournal: Sci Adv / Year: 2024
Title: The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure.
Authors: Yoon, J. / Zhang, Y.M. / Her, C. / Grant, R.A. / Ponomarenko, A.I. / Ackermann, B.E. / Hui, T. / Lin, Y.S. / Debelouchina, G.T. / Shoulders, M.D.
History
DepositionAug 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)169,9203
Polymers169,9203
Non-polymers00
Water00
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)56,6401
Polymers56,6401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)56,6401
Polymers56,6401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)56,6401
Polymers56,6401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.840, 282.920, 116.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHRchain 'A'AA21 - 39015 - 384
12SERSERPROPROchain 'A'AA413 - 453407 - 447
13PHEPHELEULEUchain 'A'AA458 - 499452 - 493
21ASNASNTHRTHRchain 'B'BB21 - 39015 - 384
22SERSERPROPROchain 'B'BB413 - 453407 - 447
23PHEPHELEULEUchain 'B'BB458 - 499452 - 493
31ASNASNTHRTHRchain 'C'CC21 - 39015 - 384
32SERSERPROPROchain 'C'CC413 - 453407 - 447
33PHEPHELEULEUchain 'C'CC458 - 499452 - 493

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Components

#1: Protein Nucleoprotein


Mass: 56640.133 Da / Num. of mol.: 3 / Mutation: R416A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Aichi/2/1968(H3N2))
Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: I6TAH8

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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: 3.96 Å3/Da / Density % sol: 68.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 8.0, 1.33 % (w/v) polyethylene glycol monomethyl ether 2000, 0.9 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.9→48.8 Å / Num. obs: 59023 / % possible obs: 98.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 83.92 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.71
Reflection shellResolution: 2.9→2.98 Å / Num. unique obs: 4122 / CC1/2: 0.646

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.68 Å / SU ML: 0.3595 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.9332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 1995 3.39 %
Rwork0.2198 56907 -
obs0.2207 58902 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 102.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10734 0 0 0 10734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001910917
X-RAY DIFFRACTIONf_angle_d0.557414670
X-RAY DIFFRACTIONf_chiral_restr0.03781560
X-RAY DIFFRACTIONf_plane_restr0.00281932
X-RAY DIFFRACTIONf_dihedral_angle_d11.36434200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.38841360.37753837X-RAY DIFFRACTION93.64
2.97-3.050.40471400.33773992X-RAY DIFFRACTION97.13
3.05-3.140.34321390.3264033X-RAY DIFFRACTION98.51
3.14-3.240.36231410.31214038X-RAY DIFFRACTION98.93
3.24-3.360.34761420.28714064X-RAY DIFFRACTION99.01
3.36-3.490.30381440.26814082X-RAY DIFFRACTION99.23
3.5-3.650.22731430.23754083X-RAY DIFFRACTION98.85
3.65-3.850.26451440.2294097X-RAY DIFFRACTION99.55
3.85-4.090.21581430.21314107X-RAY DIFFRACTION98.95
4.09-4.40.2141390.20123929X-RAY DIFFRACTION95.76
4.4-4.850.23791450.19594131X-RAY DIFFRACTION99.33
4.85-5.550.22991450.20244169X-RAY DIFFRACTION99.47
5.55-6.980.25741470.20794163X-RAY DIFFRACTION99.31
6.98-48.680.18441470.17284182X-RAY DIFFRACTION95.52

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