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- PDB-5fml: Crystal structure of the endonuclease from the PA subunit of infl... -

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Basic information

Entry
Database: PDB / ID: 5fml
TitleCrystal structure of the endonuclease from the PA subunit of influenza B virus bound to the PB2 subunit NLS peptide
Components
  • PA SUBUNIT OF INFLUENZA B POLYMERASE
  • PB2 SUBUNIT OF INFLUENZA B POLYMERASE
KeywordsVIRAL PROTEIN / ENDONUCLEASE
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 / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting ...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 / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion 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 / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
Polymerase basic protein 2 / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA B VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuilligay, D. / Gaudon, S. / Cusack, S.
CitationJournal: Mol.Cell / Year: 2016
Title: Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains.
Authors: Thierry, E. / Guilligay, D. / Kosinski, J. / Bock, T. / Gaudon, S. / Round, A. / Pflug, A. / Hengrung, N. / El Omari, K. / Baudin, F. / Hart, D.J. / Beck, M. / Cusack, S.
History
DepositionNov 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PB2 SUBUNIT OF INFLUENZA B POLYMERASE
B: PA SUBUNIT OF INFLUENZA B POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7935
Polymers26,6522
Non-polymers1413
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-29.1 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.380, 80.850, 37.910
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide PB2 SUBUNIT OF INFLUENZA B POLYMERASE


Mass: 3318.807 Da / Num. of mol.: 1 / Fragment: NLS PEPTIDE RESIDUES 742-770 / Source method: obtained synthetically / Source: (synth.) INFLUENZA B VIRUS / References: UniProt: Q5V8X3
#2: Protein PA SUBUNIT OF INFLUENZA B POLYMERASE


Mass: 23333.469 Da / Num. of mol.: 1 / Fragment: ENDONUCLEASE DOMAIN RESIDUES 1-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS / Strain: B/MEMPHIS/13/2003/ / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: Q5V8Z9
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGLYCEROL (GOL): CRYOPROTECTANT MAGNESIUM ION (MG): BOUND AT ACTIVE SITE
Sequence detailsADDITIONAL MGSMA AT N-TERMINUS. MUTATION A55S

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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: 2.7 Å3/Da / Density % sol: 54.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.5, 25% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22279 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.72 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.68
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.84 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4WRT

4wrt


Resolution: 1.7→40.42 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.671 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27556 1098 4.9 %RANDOM
Rwork0.22435 ---
obs0.22677 21181 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.895 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0.27 Å2
2--0.48 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 8 101 1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191851
X-RAY DIFFRACTIONr_bond_other_d0.0020.021752
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9682500
X-RAY DIFFRACTIONr_angle_other_deg0.96934061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44425.60491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26715360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.068159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022122
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02411
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_it2.353.004903
X-RAY DIFFRACTIONr_mcbond_other2.353902
X-RAY DIFFRACTIONr_mcangle_it3.4484.4841141
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2353.45948
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 95 -
Rwork0.345 1460 -
obs--91.2 %

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