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- PDB-3wi0: P453H/I471T mutant of PB2 middle domain from influenza virus A/Pu... -

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Basic information

Entry
Database: PDB / ID: 3wi0
TitleP453H/I471T mutant of PB2 middle domain from influenza virus A/Puerto Rico/8/34(H1N1)
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / influenza A virus / PB2 / middle domain / cap binding
Function / homology
Function and homology information


cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis ...cRNA Synthesis / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / vRNP Assembly / Viral Messenger RNA Synthesis / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / Viral mRNA Translation / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.998 Å
AuthorsTsurumura, T. / Yoshida, T. / Tsuge, H.
CitationJournal: Plos One / Year: 2013
Title: Conformational Polymorphism of m7GTP in Crystal Structure of the PB2 Middle Domain from Human Influenza A Virus
Authors: Tsurumura, T. / Qiu, H. / Yoshida, T. / Tsumori, Y. / Hatakeyama, D. / Kuzuhara, T. / Tsuge, H.
History
DepositionSep 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / 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

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Assembly

Deposited unit
A: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)19,6361
Polymers19,6361
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.818, 107.818, 136.615
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-522-

HOH

31A-619-

HOH

41A-666-

HOH

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Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 19635.779 Da / Num. of mol.: 1 / Fragment: middle domain of PB2, UNP residues 318-484 / Mutation: P453H, I471T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03428
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.2M NaCl, 2.5% (v/v) ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.998→20.98 Å / Num. obs: 20909 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.57 Å2
Reflection shellResolution: 1.998→2.09 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQZ

2vqz


Resolution: 1.998→20.975 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1222 9.66 %
Rwork0.1824 --
obs0.1868 20877 99.83 %
all-20878 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.41 Å2 / Biso mean: 39.5433 Å2 / Biso min: 12.48 Å2 / Baniso 13: 40.8734 Å2
Refinement stepCycle: LAST / Resolution: 1.998→20.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 0 185 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071363
X-RAY DIFFRACTIONf_angle_d1.0321824
X-RAY DIFFRACTIONf_dihedral_angle_d16.037525
X-RAY DIFFRACTIONf_chiral_restr0.076204
X-RAY DIFFRACTIONf_plane_restr0.005235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9975-2.04740.3181490.26691294144398
2.0474-2.10270.29441390.247513251464100
2.1027-2.16460.24171360.216513591495100
2.1646-2.23430.26621440.206713091453100
2.2343-2.31410.22961450.201313451490100
2.3141-2.40660.23671430.196313621505100
2.4066-2.5160.21781380.181113271465100
2.516-2.64840.23431410.183213401481100
2.6484-2.8140.26191480.217113311479100
2.814-3.03060.23621390.198213581497100
3.0306-3.33450.251460.190613611507100
3.3345-3.81450.22591430.162613631506100
3.8145-4.79640.18591430.148913751518100
4.7964-20.97620.21211630.172814111574100
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)
15.91333.0012-0.64757.0582-3.00113.2332-0.09960.1943-0.1297-0.67160.23940.940.6289-1.1836-0.08620.4359-0.058-0.00640.4952-0.10350.420940.6185-19.482-1.3016
24.49582.7621-5.96847.727-1.72188.6309-0.02120.19270.2367-0.11610.04640.08910.2745-0.76960.02610.3623-0.0123-0.03770.28960.01840.235249.006-11.3038-10.0768
32.37781.58410.57725.3564-2.26286.2121-0.08110.03870.03890.7197-0.21060.68130.1278-0.5860.19930.46-0.17290.1730.4013-0.1390.324744.1278-19.37238.8005
44.03820.03320.69982.9892-0.62128.0747-0.0393-0.0871-0.01110.0912-0.0760.04160.0304-0.40070.10560.2476-0.05230.05440.151-0.01970.253249.3835-12.7487.2223
50.9197-0.5175-0.49132.54822.50333.9530.0870.01120.1228-0.06070.229-0.2501-0.19010.1498-0.32950.2209-0.03370.0260.16250.04360.258456.1192-13.3080.5792
67.70540.9722-2.39383.5486-2.35832.56590.0946-0.4102-0.12580.4586-0.123-0.0186-0.13490.17960.03980.3388-0.04320.00590.21920.01310.206652.982-6.956218.0365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 315:345)A315 - 345
2X-RAY DIFFRACTION2chain 'A' and (resseq 346:358)A346 - 358
3X-RAY DIFFRACTION3chain 'A' and (resseq 359:369)A359 - 369
4X-RAY DIFFRACTION4chain 'A' and (resseq 370:413)A370 - 413
5X-RAY DIFFRACTION5chain 'A' and (resseq 414:458)A414 - 458
6X-RAY DIFFRACTION6chain 'A' and (resseq 459:483)A459 - 483

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