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- PDB-4cb5: Structure of Influenza A H5N1 PB2 cap-binding domain with bound c... -

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Basic information

Entry
Database: PDB / ID: 4cb5
TitleStructure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 8f)
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
Chem-93G / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.2Apr 11, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3385
Polymers18,8881
Non-polymers4504
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.170, 82.170, 54.840
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 (A/duck/Shantou/4610/2003(H5N1))
Plasmid: PET-M11 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CODONPLUS RIL / References: UniProt: Q2LG68
#2: Chemical ChemComp-93G / 9-N-(3-CARBOXY-4-HYDROXYPHENYL)KETOMETHYL-7-N-METHYLGUANINE


Mass: 343.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N6O4
#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.: 73 / 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: 2.84 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 4.3 / Details: 1M SODIUM ACETATE PH 4.3, 2.4M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 33681 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.5
Reflection shellResolution: 1.5→1.56 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.9 / % possible all: 98.9

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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: 1.5→43.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.334 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1585 1639 4.9 %RANDOM
Rwork0.12672 ---
obs0.12822 32042 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→43.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 28 73 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191365
X-RAY DIFFRACTIONr_bond_other_d0.0010.021356
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9821840
X-RAY DIFFRACTIONr_angle_other_deg0.91333105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6312360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0191514
X-RAY DIFFRACTIONr_chiral_restr0.130.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02323
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_restr4.17332721
X-RAY DIFFRACTIONr_sphericity_free7.812534
X-RAY DIFFRACTIONr_sphericity_bonded4.38452739
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 144 -
Rwork0.089 2292 -
obs--98.82 %

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