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- PDB-4q46: The second structure of Influenza B PB2 cap-binding domain comple... -

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Basic information

Entry
Database: PDB / ID: 4q46
TitleThe second structure of Influenza B PB2 cap-binding domain complex with GDP
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / cap binding
Function / homology: / Influenza RNA polymerase PB2 CAP binding domain / host cell mitochondrion / GUANOSINE-5'-DIPHOSPHATE / Polymerase basic protein 2
Function and homology information
Biological speciesinfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, Y. / Yang, Y. / Zheng, X.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The crystal structure of the PB2 cap-binding domain of influenza B virus reveals a novel cap recognition mechanism.
Authors: Liu, Y. / Yang, Y. / Fan, J. / He, R. / Luo, M. / Zheng, X.
History
DepositionApr 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 protein 2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4484
Polymers39,5622
Non-polymers8862
Water6,864381
1
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2242
Polymers19,7811
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2242
Polymers19,7811
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.074, 88.543, 52.151
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polymerase basic protein 2


Mass: 19780.828 Da / Num. of mol.: 2 / Fragment: cap-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) influenza B virus / Strain: B/Jiangxi/BV/2006 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J9X1Z6*PLUS
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP AT THE ...THIS SEQUENCE IS FROM INFLUENZA B VIRUS (B/JIANGXI/BV/2006) WHICH WAS NOT SUBMITTED IN UNP AT THE TIME OF PROCESSING. N-TERMINAL GSHM WERE FROM VECTOR SEQUENCE.

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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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.2M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2014
RadiationMonochromator: Crystallogic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.8→24.57 Å / Num. all: 35055 / Num. obs: 33162 / % possible obs: 94.6 % / Observed criterion σ(I): 8.5 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.217 / % possible all: 98.2

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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: 4ORO

4oro


Resolution: 1.8→24.57 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.908 / SU B: 2.28 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23065 1658 5 %RANDOM
Rwork0.16998 ---
obs0.17301 31459 94.38 %-
all-33332 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.719 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 56 381 3097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222768
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.171.9893708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64723.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.53315551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5321528
X-RAY DIFFRACTIONr_chiral_restr0.1680.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022048
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_it1.4451.51613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.51822584
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.89131155
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.3424.51122
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: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 117 -
Rwork0.205 2270 -
obs--94.91 %

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