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- PDB-4es5: Crystal structure of the cap-binding domain of polymerase basic p... -

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Basic information

Entry
Database: PDB / ID: 4es5
TitleCrystal structure of the cap-binding domain of polymerase basic protein 2 from influenza virus A/Bar-headed Gs/Qinghai/15c/2005 (h5n1) with bound m7GTP
ComponentsPolymerase basic subunit 2
KeywordsTRANSCRIPTION / cap-binding protein
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMeng, G. / Liu, Y. / Zheng, X.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and functional characterization of K339T substitution identified in the PB2 subunit cap-binding pocket of influenza A virus
Authors: Liu, Y. / Qin, K. / Meng, G. / Zhang, J. / Zhou, J. / Zhao, G. / Luo, M. / Zheng, X.
History
DepositionApr 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
C: Polymerase basic subunit 2
D: Polymerase basic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,23812
Polymers76,6974
Non-polymers2,5418
Water10,413578
1
A: Polymerase basic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8093
Polymers19,1741
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase basic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8093
Polymers19,1741
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase basic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8093
Polymers19,1741
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase basic subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8093
Polymers19,1741
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.480, 39.100, 141.080
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Polymerase basic subunit 2


Mass: 19174.193 Da / Num. of mol.: 4 / Fragment: CAP-BINDING DOMAIN, UNP RESIDUES 317-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: 05(H5N1) / Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4FAV8, UniProt: Q4FAU9*PLUS
#2: Chemical
ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Ammonium sulfate, 0.01M Magnesium chloride, 0.05M MES pH5.6, 22% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→14.91 Å / Num. all: 63747 / Num. obs: 63747 / % possible obs: 99.1 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VQZ

2vqz


Resolution: 1.8→14.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.609 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28495 3153 5.1 %RANDOM
Rwork0.19724 ---
obs0.20166 59069 99.71 %-
all-62212 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.436 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.01 Å2
2--0.16 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5148 0 152 578 5878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225388
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.9887274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68623.223242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.561151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.011554
X-RAY DIFFRACTIONr_chiral_restr0.1540.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023918
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.8311.53235
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.74825233
X-RAY DIFFRACTIONr_scbond_it3.87432153
X-RAY DIFFRACTIONr_scangle_it5.5014.52041
X-RAY DIFFRACTIONr_rigid_bond_restr2.48735388
X-RAY DIFFRACTIONr_sphericity_free10.4893578
X-RAY DIFFRACTIONr_sphericity_bonded6.06635311
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 210 -
Rwork0.25 4312 -
obs--99.74 %

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