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- PDB-2ztt: Crystal Structure of RNA polymerase PB1-PB2 subunits from Influen... -

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Basic information

Entry
Database: PDB / ID: 2ztt
TitleCrystal Structure of RNA polymerase PB1-PB2 subunits from Influenza A Virus
Components
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsTRANSFERASE / Influenza virus / RNA polymerase / PB1-PB2 complex form / Nucleotide-binding / Nucleotidyltransferase / Nucleus / RNA replication / RNA-directed RNA polymerase / Mitochondrion / mRNA capping / mRNA processing / 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 / viral transcription / 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 / host cell cytoplasm / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding / extracellular region
Similarity search - Function
Helix Hairpins - #720 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / : / : / : ...Helix Hairpins - #720 / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / : / : / : / 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 / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSugiyama, K. / Obayashi, E. / Park, S.-Y.
CitationJournal: Embo J. / Year: 2009
Title: Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase
Authors: Sugiyama, K. / Obayashi, E. / Kawaguchi, A. / Suzuki, Y. / Tame, J.R.H. / Nagata, K. / Park, S.-Y.
History
DepositionOct 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase catalytic subunit
B: Polymerase basic protein 2
C: RNA-directed RNA polymerase catalytic subunit
D: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)28,6394
Polymers28,6394
Non-polymers00
Water59433
1
A: RNA-directed RNA polymerase catalytic subunit
B: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)14,3192
Polymers14,3192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area7250 Å2
MethodPISA
2
C: RNA-directed RNA polymerase catalytic subunit
D: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)14,3192
Polymers14,3192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-27 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.273, 61.477, 45.473
Angle α, β, γ (deg.)90.00, 103.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA-directed RNA polymerase catalytic subunit / RNA polymerase PB1 subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 9588.427 Da / Num. of mol.: 2 / Fragment: PB1 C-terminal fragment, UNP residues 679-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/34(H1N1))
Gene: PB1 / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B824(DE3)codonplus / References: UniProt: P03431, RNA-directed RNA polymerase
#2: Protein/peptide Polymerase basic protein 2 / RNA polymerase PB2 subunit / RNA-directed RNA polymerase subunit P3


Mass: 4731.061 Da / Num. of mol.: 2 / Fragment: PB2 N-terminal ragment, UNP residues 1-37
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/34(H1N1))
Gene: PB2 / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)codonplus / References: UniProt: P03428
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M potassium phosphate, 15% PEG 4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97898,0.97931,0.9832
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2008 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979311
30.98321
ReflectionResolution: 2.1→50 Å / Num. all: 13052 / Num. obs: 13052 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.131 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.532 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.299 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27164 633 4.9 %RANDOM
Rwork0.2324 ---
obs0.23452 12352 100 %-
all-12352 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.199 Å2
Baniso -1Baniso -2Baniso -3
1-5.7 Å20 Å27.1 Å2
2---3.97 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 0 33 1830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221815
X-RAY DIFFRACTIONr_angle_refined_deg2.0661.9752411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73122.18487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.2715393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6981525
X-RAY DIFFRACTIONr_chiral_restr0.1380.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021307
X-RAY DIFFRACTIONr_nbd_refined0.2710.2880
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.22
X-RAY DIFFRACTIONr_mcbond_it1.5931.51135
X-RAY DIFFRACTIONr_mcangle_it2.25921764
X-RAY DIFFRACTIONr_scbond_it3.9843766
X-RAY DIFFRACTIONr_scangle_it5.5164.5647
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 43 -
Rwork0.306 841 -
obs--100 %

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