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- PDB-4u6o: STRUCTURE OF THE CAP-BINDING DOMAIN OF INFLUENZA VIRUS POLYMERASE... -

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Basic information

Entry
Database: PDB / ID: 4u6o
TitleSTRUCTURE OF THE CAP-BINDING DOMAIN OF INFLUENZA VIRUS POLYMERASE SUBUNIT PB2
ComponentsPolymerase basic protein 2
KeywordsTRANSCRIPTION / RNA-DEPENDENT RNA POLYMERASE / PB2 SUBUNIT / INFLUENZA VIRUS / CAP-BINDING DOMAIN
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 / Viral Messenger RNA Synthesis / vRNP Assembly / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / host cell mitochondrion / Viral mRNA Translation / 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 / 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 helical domain / Influenza RNA polymerase PB2 CAP binding domain
Similarity search - Domain/homology
PHOSPHATE ION / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsFukushima, K. / Takimoto-Kamimura, M.
CitationJournal: To Be Published
Title: STRUCTURE OF THE CAP-BINDING DOMAIN OF INFLUENZA VIRUS POLYMERASE SUBUNIT PB2
Authors: Fukushima, K. / Takimoto-Kamimura, M.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase basic protein 2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9684
Polymers37,7782
Non-polymers1902
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-17 kcal/mol
Surface area15930 Å2
2
B: Polymerase basic protein 2
hetero molecules

A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9684
Polymers37,7782
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area1470 Å2
ΔGint-22 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.218, 64.377, 64.765
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18889.006 Da / Num. of mol.: 2 / Fragment: UNP residues 318-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03428
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1mM Na-Malonate(pH7.0), 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 74594 / % possible obs: 97 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Χ2: 0.919 / Net I/av σ(I): 19.695 / Net I/σ(I): 12 / Num. measured all: 285961
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.323.80.48836340.98294.6
1.32-1.353.80.43736710.99495.6
1.35-1.373.80.38936350.99295.5
1.37-1.43.80.33736710.96995.6
1.4-1.433.80.28636840.99196.4
1.43-1.463.80.23936730.99595.4
1.46-1.53.80.20436971.01397.1
1.5-1.543.80.17336881.06396.3
1.54-1.593.80.15437001.06596.5
1.59-1.643.80.12537380.97497.9
1.64-1.73.80.10437490.89297.4
1.7-1.763.90.08537090.8197.3
1.76-1.843.80.0737790.71797.7
1.84-1.943.90.06337450.74898.1
1.94-2.063.90.06437960.95798.5
2.06-2.223.90.05838030.90598.7
2.22-2.453.90.05237880.71698.7
2.45-2.83.90.05138450.70599.2
2.8-3.533.80.05338470.82799.2
3.53-503.70.05937421.10794.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.2.0019refinement
PDB_EXTRACT3.14data extraction
HKLdata scaling
RefinementResolution: 1.3→38.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.958 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 3489 5 %RANDOM
Rwork0.2089 66068 --
obs0.2099 69557 90.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.81 Å2 / Biso mean: 18.594 Å2 / Biso min: 10.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.03 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.3→38.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 10 258 2823
Biso mean--25.59 30.89 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222817
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.9633812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7655375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06222.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94215576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6091536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022112
X-RAY DIFFRACTIONr_nbd_refined0.1680.21218
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0710.2250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.227
X-RAY DIFFRACTIONr_mcbond_it0.3661.51802
X-RAY DIFFRACTIONr_mcangle_it0.6322795
X-RAY DIFFRACTIONr_scbond_it0.76131153
X-RAY DIFFRACTIONr_scangle_it1.1654.5995
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 95 -
Rwork0.233 2138 -
all-2233 -
obs--39.49 %

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