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- PDB-3a1g: High-Resolution Crystal Structure of RNA polymerase PB1-PB2 subun... -

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Basic information

Entry
Database: PDB / ID: 3a1g
TitleHigh-Resolution Crystal 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 / 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 / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus ...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 / vRNA Synthesis / Viral RNP Complexes in the Host Cell Nucleus / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / Viral Messenger RNA Synthesis / vRNP Assembly / cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / Viral mRNA Translation / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / host cell cytoplasm / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / 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 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : ...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 C-terminal domain / : / Influenza RNA polymerase PB2 6th 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSugiyama, K. / Park, S.-Y. / Obayashi, E.
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
DepositionApr 2, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,8134
Polymers28,8134
Non-polymers00
Water1,13563
1
A: RNA-directed RNA polymerase catalytic subunit
B: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)14,4072
Polymers14,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-27 kcal/mol
Surface area6930 Å2
MethodPISA
2
C: RNA-directed RNA polymerase catalytic subunit
D: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)14,4072
Polymers14,4072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-27 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.701, 69.987, 61.348
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 9675.504 Da / Num. of mol.: 2 / Fragment: PB1 C-terminal fragment, UNP residues 678-757
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/34(H1N1))
Strain: strain A/Puerto Rico/8/1934 H1N1 / Gene: PB1 / Plasmid: modified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILcodonPlus / 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))
Strain: strain A/Puerto Rico/8/1934 H1N1 / Gene: PB2 / Plasmid: midified pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RILcodonPlus / References: UniProt: P03428
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 80mM Sodium Citrate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 25865 / Num. obs: 25865 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 25 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZTT

2ztt


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / SU B: 2.709 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28967 1315 5.1 %RANDOM
Rwork0.2377 ---
all0.24039 25865 --
obs0.24039 24512 100 %-
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: 36.543 Å2
Baniso -1Baniso -2Baniso -3
1-4.34 Å20 Å20.7 Å2
2---2.46 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 63 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221844
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9752448
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7345218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83522.04588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1715400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6531526
X-RAY DIFFRACTIONr_chiral_restr0.1460.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021332
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.2948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21291
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5031.51152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16421792
X-RAY DIFFRACTIONr_scbond_it3.7293777
X-RAY DIFFRACTIONr_scangle_it4.9064.5656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 69 -
Rwork0.235 1399 -
obs--100 %

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