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- PDB-4cb6: Structure of Influenza A H5N1 PB2 cap-binding domain with bound c... -

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Basic information

Entry
Database: PDB / ID: 4cb6
TitleStructure of Influenza A H5N1 PB2 cap-binding domain with bound cap analogue (compound 11)
ComponentsPOLYMERASE BASIC SUBUNIT 2
KeywordsTRANSFERASE / INFLUENZA POLYMERASE / M7GTP / 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
2,9-N,N-DI(4-CARBOXYBUTYL)-7-N-METHYLGUANINE / IODIDE ION / Polymerase basic protein 2
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)40,15817
Polymers37,7762
Non-polymers2,38315
Water2,594144
1
A: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1439
Polymers18,8881
Non-polymers1,2558
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE BASIC SUBUNIT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0168
Polymers18,8881
Non-polymers1,1287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.170, 31.130, 98.790
Angle α, β, γ (deg.)90.00, 118.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18887.951 Da / Num. of mol.: 2 / 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-29R / 2,9-N,N-DI(4-CARBOXYBUTYL)-7-N-METHYLGUANINE


Mass: 366.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N5O5
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsIODIDE ION (IOD): 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: 2.09 Å3/Da / Density % sol: 41.2 % / Description: NONE
Crystal growpH: 6.3 / Details: 0.2 M AMMONIUM IODIDE, PH 6.3, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 24866 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 2.95 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.6 / % possible all: 98.5

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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: 1.9→45.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.405 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 1268 5.1 %RANDOM
Rwork0.21141 ---
obs0.21466 23598 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.847 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.02 Å2
2---0.19 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 65 144 2789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192689
X-RAY DIFFRACTIONr_bond_other_d0.0050.022672
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9793609
X-RAY DIFFRACTIONr_angle_other_deg1.05236121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9695328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47222.893121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83115511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7811529
X-RAY DIFFRACTIONr_chiral_restr0.0930.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023019
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02636
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 89 -
Rwork0.293 1734 -
obs--97.91 %

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