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- PDB-4cb7: Structure of Influenza A H5N1 PB2 cap-binding domain with bound c... -

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Basic information

Entry
Database: PDB / ID: 4cb7
TitleStructure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 8e)
ComponentsPOLYMERASE BASIC SUBUNIT 2
KeywordsTRANSCRIPTION / 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
Chem-41G / Polymerase basic protein 2
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
B: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2097
Polymers36,4962
Non-polymers7135
Water2,324129
1
A: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4323
Polymers18,2481
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7774
Polymers18,2481
Non-polymers5283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.940, 108.180, 39.050
Angle α, β, γ (deg.)90.00, 91.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18248.199 Da / Num. of mol.: 2 / Fragment: CAP-BINDING DOMAIN, RESIDUES 318-483 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: LOOP DELETION VARIANT / Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/DUCK/SHANTOU/4610/2003(H5N1) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS RIL / References: UniProt: Q2LG68
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-41G / 5-[2-(2-azanyl-7-methyl-6-oxidanylidene-1H-purin-9-ium-9-yl)ethanoyl]-2-oxidanyl-benzoic acid


Mass: 344.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N5O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsEXTRA N-TERMINAL GLYCINE AFTER HIS-TAG CLEAVAGE LOOP DELETION VARIANT 420-FVNRANQRLNP REPLACED BY 420-FGSGLNP

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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: 2.07 Å3/Da / Density % sol: 40.7 % / Description: NONE
Crystal growpH: 6.3 / Details: 0.2M AMMONIUM NITRATE, PH 6.3, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9749
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 25819 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.29 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3
Reflection shellResolution: 1.85→1.94 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / % possible all: 99.7

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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: 1.85→36.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.968 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 1313 5.1 %RANDOM
Rwork0.17118 ---
obs0.17336 24506 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.504 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20.3 Å2
2--0.04 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 49 129 2628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192583
X-RAY DIFFRACTIONr_bond_other_d0.0010.022573
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9823476
X-RAY DIFFRACTIONr_angle_other_deg0.77135913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27623.119109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35215492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9361524
X-RAY DIFFRACTIONr_chiral_restr0.0940.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 82 -
Rwork0.221 1813 -
obs--99.79 %

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