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- PDB-4cb4: Structure of Influenza A H5N1 PB2 cap-binding domain with bound m7GTP -

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Basic information

Entry
Database: PDB / ID: 4cb4
TitleStructure of Influenza A H5N1 PB2 cap-binding domain with bound m7GTP
ComponentsPOLYMERASE BASIC SUBUNIT 2
KeywordsTRANSFERASE / CAP-BINDING INHIBITORS
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding
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 polymerase PB2 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
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Polymerase basic protein 2
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPautus, S. / Sehr, P. / Lewis, J. / Fortune, A. / Wolkerstorfer, A. / Szolar, O. / Gulligay, D. / Lunardi, T. / Decout, J.L. / Cusack, S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: New 7-Methyl-Guanosine Derivatives Targeting the Influenza Polymerase Pb2 CAP-Binding Domain
Authors: Pautus, S. / Sehr, P. / Lewis, J. / Fortune, A. / Wolkerstorfer, A. / Szolar, O. / Gulligay, D. / Lunardi, T. / Decout, J.L. / Cusack, S.
History
DepositionOct 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5345
Polymers18,8881
Non-polymers6464
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.480, 82.480, 55.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein POLYMERASE BASIC SUBUNIT 2 / H5N1 INFLUENZA POLYMERASE PB2 SUBUNIT


Mass: 18887.951 Da / Num. of mol.: 1 / Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/DUCK/SHANTOU/4610/2003(H5N1) / Plasmid: PET-M11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL / References: UniProt: Q2LG68
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCHLORIDE ION (CL): FROM CRYSTALLISATION MEDIUM
Sequence detailsEXTRA N-TERMINAL GLYCINE AFTER HIS-TAG CLEAVAGE

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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: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.1M SODIUM ACETATE PH 4.6, 2M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 28140 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.72 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.62
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.52 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQZ

2vqz


Resolution: 1.6→43.35 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.62 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 1387 4.9 %RANDOM
Rwork0.12585 ---
obs0.12798 26753 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.08 Å20 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 36 232 1553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191449
X-RAY DIFFRACTIONr_bond_other_d0.0010.021422
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9921967
X-RAY DIFFRACTIONr_angle_other_deg0.7593.0023252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.44822.81364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1715281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7361516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021661
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.41632871
X-RAY DIFFRACTIONr_sphericity_free29.999558
X-RAY DIFFRACTIONr_sphericity_bonded8.19753017
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 98 -
Rwork0.179 1974 -
obs--98.76 %

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