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- PDB-7nt8: Influenza virus H3N2 nucleoprotein - R416A mutant -

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Basic information

Entry
Database: PDB / ID: 7nt8
TitleInfluenza virus H3N2 nucleoprotein - R416A mutant
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme,Nucleoprotein
KeywordsRNA BINDING PROTEIN / Influenza virus / nucleoprotein / RNA-binding protein
Function / homology
Function and homology information


helical viral capsid / glutathione transferase / glutathione transferase activity / glutathione metabolic process / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus ...helical viral capsid / glutathione transferase / glutathione transferase activity / glutathione metabolic process / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / Nucleoprotein
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKeown, J.R. / Knight, M.L. / Grimes, J.M. / Fodor, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R009945/1 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structure of an H3N2 influenza virus nucleoprotein.
Authors: Knight, M.L. / Fan, H. / Bauer, D.L.V. / Grimes, J.M. / Fodor, E. / Keown, J.R.
History
DepositionMar 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: 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_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme,Nucleoprotein
B: Glutathione S-transferase class-mu 26 kDa isozyme,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)165,7782
Polymers165,7782
Non-polymers00
Water91951
1
A: Glutathione S-transferase class-mu 26 kDa isozyme,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)82,8891
Polymers82,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase class-mu 26 kDa isozyme,Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)82,8891
Polymers82,8891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.775, 63.376, 105.950
Angle α, β, γ (deg.)90.000, 98.318, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,Nucleoprotein / GST 26 / Sj26 antigen / SjGST / Nucleocapsid protein / Protein N


Mass: 82888.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Influenza A virus (A/Northern Territory/60/1968(H3N2))
Gene: NP / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: Q1AR08, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M of each alcohol (1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2- propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol) ...Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M of each alcohol (1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2- propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol), 0.1 M MES/imidazole pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.22→86.85 Å / Num. obs: 38053 / % possible obs: 90.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.09 Å2 / CC1/2: 0.992 / Net I/σ(I): 8.1
Reflection shellResolution: 2.22→2.3 Å / Num. unique obs: 203 / CC1/2: 0.51 / % possible all: 55.8

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Processing

Software
NameVersionClassification
PHENIX1.18rc2_3794refinement
PHASERphasing
XDSdata processing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZDP

3zdp


Resolution: 2.22→86.85 Å / SU ML: 0.2667 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.6091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2648 1830 4.81 %
Rwork0.2122 36223 -
obs0.2147 38053 66.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.97 Å2
Refinement stepCycle: LAST / Resolution: 2.22→86.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6762 0 0 51 6813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316875
X-RAY DIFFRACTIONf_angle_d0.53549232
X-RAY DIFFRACTIONf_chiral_restr0.0373980
X-RAY DIFFRACTIONf_plane_restr0.00291212
X-RAY DIFFRACTIONf_dihedral_angle_d15.0075958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.334660.2455108X-RAY DIFFRACTION2.63
2.28-2.350.3428200.2709432X-RAY DIFFRACTION10.43
2.35-2.430.3555430.299891X-RAY DIFFRACTION21.43
2.43-2.510.2729630.30471398X-RAY DIFFRACTION33.49
2.51-2.610.3321720.29581909X-RAY DIFFRACTION45.61
2.61-2.730.36721500.29782713X-RAY DIFFRACTION65.28
2.73-2.880.31781870.27813592X-RAY DIFFRACTION86.48
2.88-3.060.29261990.27584128X-RAY DIFFRACTION99.06
3.06-3.290.31342110.25464175X-RAY DIFFRACTION99.95
3.29-3.620.29592200.21754177X-RAY DIFFRACTION99.98
3.62-4.150.26712130.18344187X-RAY DIFFRACTION99.77
4.15-5.220.21272000.17324237X-RAY DIFFRACTION99.78
5.23-86.850.22962460.18564276X-RAY DIFFRACTION99.49
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.54959020347-0.0560652944336-0.07088775130733.35036467804-0.8445401566162.16354703861-0.1066521571670.3923484605711.209800579780.0408679827485-0.139111598122-0.305517377877-0.2558328595080.3432910420350.1756868436520.297760433304-0.0778077313778-0.07298649056250.3689665139220.1711070515130.59692775684111.33878755368.6870556537410.1541195652
23.08953043399-0.3662922282220.7439967766253.09526979917-1.789980656164.94662401380.3436650913320.885948671046-0.73157747809-0.601734910588-0.08786863716920.3280437017020.729803613280.24710391953-0.06434588150740.4231315181410.04742005731760.07230441932030.772504047295-0.007773441186230.68163893850210.6424834209-4.52879717711.93862316506
33.790483806170.1129519260860.464196011942.39308685521-1.157958941922.25912610539-0.092551944820.7656119648980.657854806369-0.226215002996-0.105826813357-0.265487013999-0.06960361292490.4117624069040.2981608250430.326665729547-0.0003514552296450.002830513860290.3745581403930.1258241372810.3962582685911.63656203152.422840126118.42375604841
45.128588364021.61738124417-0.6117136125573.26833409551-0.466079117632.16996181238-0.0976363650097-0.279078916237-0.1662978657210.150442821216-0.0926046547921-0.3974292547130.1124342765850.122224914540.09928560081210.2632618023790.0511821801933-0.01180775502520.311140605502-0.02151578653470.347626707153-2.36376323003-5.4417724474621.0689386779
54.782046285211.66684923491-0.8602119030734.14259477639-1.946899071784.79842878687-0.0631395308651-0.6454700116970.1718832384140.419695031449-0.03979492303080.1241456763910.0503816309932-0.07730378540670.08611252309490.1762115794340.138686506121-0.04977128097240.428549335554-0.1248523803580.429588768258-13.4895853325-4.4651799669425.6287167375
65.576716179361.42373290247-0.4038306376395.590913228951.996815411213.08645782296-0.0812483112093-0.5794017615861.195297909730.266841709632-0.1644109810031.17507639656-0.471736391245-0.03951344628090.2390445889560.5307873621440.02280172052430.002131091397250.4971655990850.04035091910510.709767926738-12.9658730297.7700420449922.8224260471
74.68624320509-0.5835092708110.3571987955863.562488155460.3248118046193.095256903340.03105224839280.344124519724-0.610636929106-0.3675349542510.07196715461210.5011665105230.144859882579-0.202310264671-0.02539236962110.263371419746-0.0124791265872-0.00322184469940.2823173765080.03712785023260.32633251799834.3997299057-13.987416577618.262127909
83.86019867021-1.74054944007-0.8475932641253.69562956945-0.9670542230922.0580017461-0.1131350618350.3904398458210.0177007901817-0.4945407044350.192750270250.301917600049-0.416585662162-0.12725721424-0.1369433747130.4694967171520.00567919680324-0.00988722227910.3175133047640.002575411318650.33046042092144.900656300510.697063957223.6576832641
92.806596617150.3115960582660.08683140404722.10346785658-0.05508824345751.75041183909-0.0615067584427-0.399920016698-0.08558887965470.2511257831730.1009719147470.120029712846-0.1873082484760.014033049937-0.04210161788870.3687782509090.05031733115020.05648063192850.4297725189550.03323559190620.23118540746244.0957573382-3.4052064566134.4961675038
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 72 )AA21 - 721 - 52
22chain 'A' and (resid 73 through 102 )AA73 - 10253 - 82
33chain 'A' and (resid 103 through 147 )AA103 - 14783 - 127
44chain 'A' and (resid 148 through 370 )AA148 - 370128 - 350
55chain 'A' and (resid 371 through 450 )AA371 - 450351 - 402
66chain 'A' and (resid 451 through 497 )AA451 - 497403 - 439
77chain 'B' and (resid 20 through 147 )BB20 - 1471 - 125
88chain 'B' and (resid 148 through 208 )BB148 - 208126 - 186
99chain 'B' and (resid 209 through 497 )BB209 - 497187 - 419

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