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- PDB-3cw4: Large c-terminal domain of influenza a virus RNA-dependent polyme... -

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Basic information

Entry
Database: PDB / ID: 3cw4
TitleLarge c-terminal domain of influenza a virus RNA-dependent polymerase PB2
ComponentsPolymerase basic protein 2
KeywordsTRANSFERASE / RNA polymerase / Mitochondrion / mRNA capping / mRNA processing / Nucleus / Virion
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 / Viral mRNA Translation / host cell mitochondrion / 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
Polymerase Basic Protein 2, C-terminal 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 ...Polymerase Basic Protein 2, C-terminal 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 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKuzuhara, T. / Kise, D. / Yoshida, H. / Horita, T. / Murasaki, Y. / Utsunomiya, H. / Fujiki, H. / Tsuge, H.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis of the influenza A virus RNA polymerase PB2 RNA-binding domain containing the pathogenicity-determinant lysine 627 residue
Authors: Kuzuhara, T. / Kise, D. / Yoshida, H. / Horita, T. / Murazaki, Y. / Nishimura, A. / Echigo, N. / Utsunomiya, H. / Tsuge, H.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Database references
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


Theoretical massNumber of molelcules
Total (without water)25,2951
Polymers25,2951
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.527, 52.527, 156.357
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 25295.215 Da / Num. of mol.: 1 / Fragment: Large c-terminal domain PB2, UNP residues 535-759
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Plasmid details: plasmid / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P03428, Transferases; Transferring phosphorus-containing groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.2M formate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.07172, 1.07204, 1.05382
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.071721
21.072041
31.053821
ReflectionResolution: 2.7→50 Å / Num. all: 7319 / Num. obs: 7328 / % possible obs: 98.8 % / Observed criterion σ(I): 1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→34.27 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.884 / SU B: 15.07 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 5.141 / ESU R Free: 0.399 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29041 335 4.6 %RANDOM
Rwork0.23741 ---
obs0.23995 6940 98.74 %-
all-7319 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.776 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å21.28 Å20 Å2
2--2.57 Å20 Å2
3----3.85 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 0 86 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221674
X-RAY DIFFRACTIONr_bond_other_d0.0020.021554
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.9572260
X-RAY DIFFRACTIONr_angle_other_deg2.08833617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0875207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021842
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02339
X-RAY DIFFRACTIONr_nbd_refined0.2540.2494
X-RAY DIFFRACTIONr_nbd_other0.2710.22013
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.21072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2181.51032
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9221668
X-RAY DIFFRACTIONr_scbond_it1.9983642
X-RAY DIFFRACTIONr_scangle_it3.4854.5592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.772 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.505 19
Rwork0.314 513

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