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

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Basic information

Entry
Database: PDB / ID: 8twr
TitleInfluenza A virus (A/Aichi/2/1968(H3N2) nucleoprotein mutant - 2-7 deleted, P283S, 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 / molecular replacement / Resolution: 3.09 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

Downloads & links

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Assembly

Deposited unit
C: Nucleoprotein
A: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,9134
Polymers169,8903
Non-polymers231
Water00
1
A: Nucleoprotein
B: Nucleoprotein
hetero molecules

C: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)169,9134
Polymers169,8903
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
Buried area6000 Å2
ΔGint-36 kcal/mol
Surface area60280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.420, 285.220, 116.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 451 or (resid 452...
21(chain B and (resid 21 through 453 or resid 459 through 499))
31chain C

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
11ASNASNALAALA(chain A and (resid 21 through 451 or (resid 452...AB21 - 45115 - 445
12LYSLYSLYSLYS(chain A and (resid 21 through 451 or (resid 452...AB452446
13ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
14ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
15ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
16ASNASNLEULEU(chain A and (resid 21 through 451 or (resid 452...AB21 - 49915 - 493
21ASNASNPROPRO(chain B and (resid 21 through 453 or resid 459 through 499))BC21 - 45315 - 447
22GLNGLNLEULEU(chain B and (resid 21 through 453 or resid 459 through 499))BC459 - 499453 - 493
31ASNASNLEULEUchain CCA21 - 49915 - 493

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Components

#1: Protein Nucleoprotein


Mass: 56630.102 Da / Num. of mol.: 3 / Mutation: P283S, 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
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestN

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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: 4.01 Å3/Da / Density % sol: 69.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 8.0, 1.01 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: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.09→48.92 Å / Num. obs: 50131 / % possible obs: 99.6 % / Redundancy: 8.532 % / Biso Wilson estimate: 81.083 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.151 / Χ2: 0.883 / Net I/σ(I): 12.76 / Num. measured all: 427717 / Scaling rejects: 1190
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.09-3.177.2321.3232.1425333366635030.691.42395.6
3.17-3.267.8991.093.1828264358035780.8321.16699.9
3.26-3.358.4160.8684.0629640352235220.8990.923100
3.35-3.469.2010.7264.9830796334733470.9330.769100
3.46-3.579.1490.5186.5730284331033100.9630.549100
3.57-3.699.0960.417.8428808316731670.9730.435100
3.69-3.839.0370.3029.4627880308530850.9850.32100
3.83-3.998.8920.22811.5226417297229710.9880.242100
3.99-4.178.790.17413.6524965284128400.9920.185100
4.17-4.378.5940.15114.4823418272527250.9930.161100
4.37-4.618.3140.13415.6921626260226010.9940.142100
4.61-4.897.4110.10816.8518224246324590.9950.11699.8
4.89-5.238.9960.1118.8920799231223120.9970.116100
5.23-5.649.0780.10519.7719754217621760.9960.112100
5.64-6.188.9840.12017942199719970.9960.106100
6.18-6.918.7130.08522.7615953183118310.9970.09100
6.91-7.988.3990.07225.9713439160016000.9980.077100
7.98-9.787.2090.05230.799985138913850.9980.05699.7
9.78-13.838.5030.04239.19260108910890.9990.045100
13.83-48.927.7880.04138.3949306526330.9990.04497.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.17.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→48.92 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2347 2005 4 %
Rwork0.2185 48076 -
obs0.2191 50081 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 286.14 Å2 / Biso mean: 97.4361 Å2 / Biso min: 50.35 Å2
Refinement stepCycle: final / Resolution: 3.09→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 1 0 10738
Biso mean--73.24 --
Num. residues----1363
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6777X-RAY DIFFRACTION3.205TORSIONAL
12B6777X-RAY DIFFRACTION3.205TORSIONAL
13C6777X-RAY DIFFRACTION3.205TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.09-3.170.44431350.39253226336195
3.17-3.250.34471440.319434183562100
3.25-3.350.35421400.298134103550100
3.35-3.460.29071420.285933853527100
3.46-3.580.27691420.260734283570100
3.58-3.730.22941380.239334263564100
3.73-3.890.24021440.226634163560100
3.89-4.10.24211430.215834313574100
4.1-4.360.22061420.216634243566100
4.36-4.690.22711460.202534613607100
4.69-5.160.20981430.196434513594100
5.16-5.910.24241480.212234733621100
5.91-7.440.21251470.20735043651100
7.44-48.920.18941510.176236233774100

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