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- PDB-5efc: Structure of Influenza B Lee PB2 cap-binding domain bound to GTP -

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Basic information

Entry
Database: PDB / ID: 5efc
TitleStructure of Influenza B Lee PB2 cap-binding domain bound to GTP
ComponentsPolymerase basic protein 2
KeywordsPROTEIN BINDING / cap-binding domain
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 / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / 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-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 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMa, X. / Shia, S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis of mRNA Cap Recognition by Influenza B Polymerase PB2 Subunit.
Authors: Xie, L. / Wartchow, C. / Shia, S. / Uehara, K. / Steffek, M. / Warne, R. / Sutton, J. / Muiru, G.T. / Leonard, V.H. / Bussiere, D.E. / Ma, X.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9652
Polymers20,4421
Non-polymers5231
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-1 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.515, 46.930, 87.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 20441.531 Da / Num. of mol.: 1 / Fragment: cap-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Strain: B/Lee/1940 / Gene: PB2 / Plasmid: pTrcHis2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QLL6
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 42% PEG400, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.9→46.93 Å / Num. obs: 13781 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 20.06 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.062 / Net I/σ(I): 10.2 / Num. measured all: 63046
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.9-24.30.7142.1846819730.38599.9
6.01-46.934.20.03924.620584910.02197.9

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Processing

Software
NameVersionClassification
Aimless3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 1.9→36.798 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 688 5.01 %
Rwork0.183 13051 -
obs0.1851 13739 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.52 Å2 / Biso mean: 28.3687 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.9→36.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 32 98 1455
Biso mean--46.82 34.51 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071382
X-RAY DIFFRACTIONf_angle_d1.1551855
X-RAY DIFFRACTIONf_chiral_restr0.048193
X-RAY DIFFRACTIONf_plane_restr0.005237
X-RAY DIFFRACTIONf_dihedral_angle_d19.389543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.04670.29811520.240925472699100
2.0467-2.25260.25541550.199525532708100
2.2526-2.57850.25421330.193825812714100
2.5785-3.24840.22251230.180926192742100
3.2484-36.80530.18421250.16212751287699
Refinement TLS params.Method: refined / Origin x: 31.8421 Å / Origin y: 39.4215 Å / Origin z: 35.0681 Å
111213212223313233
T0.0557 Å2-0.0046 Å20.0028 Å2-0.0681 Å2-0.0043 Å2--0.0628 Å2
L0.5768 °2-0.2456 °2-0.1154 °2-0.6022 °20.1044 °2--0.9104 °2
S0.0063 Å °0.0285 Å °0.0169 Å °-0.0632 Å °-0.0532 Å °-0.0216 Å °-0.0508 Å °-0.0051 Å °-0.0015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA324 - 486
2X-RAY DIFFRACTION1allL1
3X-RAY DIFFRACTION1allS1 - 98

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