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- PDB-4avl: Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in... -

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Basic information

Entry
Database: PDB / ID: 4avl
TitleInfluenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with dTMP
ComponentsPOLYMERASE PA
KeywordsHYDROLASE / ENDONUCLEASE / MANGANESE-DEPENDENT
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THYMIDINE-5'-PHOSPHATE / Polymerase acidic protein
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H.J. / Ruigrok, R.W.H. / Cusack, S.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza Ph1N1 (2009) Polymerase.
Authors: Kowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H. / Ruigrok, R.W. / Cusack, S.
History
DepositionMay 28, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.2Dec 20, 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 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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: POLYMERASE PA
B: POLYMERASE PA
C: POLYMERASE PA
D: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,48616
Polymers95,7574
Non-polymers1,72812
Water4,216234
1
A: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3714
Polymers23,9391
Non-polymers4323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3714
Polymers23,9391
Non-polymers4323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3714
Polymers23,9391
Non-polymers4323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: POLYMERASE PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3714
Polymers23,9391
Non-polymers4323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.890, 121.240, 129.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
POLYMERASE PA / POLYMERASE PA SUBUNIT


Mass: 23939.291 Da / Num. of mol.: 4 / Fragment: ENDONUCLEASE RESIDUES 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/CALIFORNIA/04/2009 (H1N1) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3W5S0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK NUMBER ACP44156

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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: 2.24 Å3/Da / Density % sol: 45.2 % / Description: NONE
Crystal growpH: 5.5
Details: 25% PEG 3350 0.1 M BIS-TRIS PH 5.5 0.2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 71829 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.02 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.22 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W69

2w69


Resolution: 1.87→41.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.232 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 3655 5.1 %RANDOM
Rwork0.19807 ---
obs0.19996 68174 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2---1.11 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.87→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6321 0 92 234 6647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.026549
X-RAY DIFFRACTIONr_bond_other_d0.0010.024628
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9598802
X-RAY DIFFRACTIONr_angle_other_deg0.88311162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4175753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79923.255341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.761151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2191559
X-RAY DIFFRACTIONr_chiral_restr0.090.2938
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021447
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: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 249 -
Rwork0.311 4648 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.339-0.1021-0.77732.0458-0.61872.785-0.0619-0.5017-0.08280.23360.06630.03170.25060.2919-0.00430.08540.0586-0.01670.1101-0.00040.029247.54875.75113.027
24.231.16140.47483.6887-0.45582.60440.02160.15290.4764-0.19910.13860.3521-0.3321-0.0743-0.16030.24350.03410.07660.07090.0050.225762.36342.5315.401
33.1-0.44380.37235.15410.25912.68330.0911-0.22090.17560.35110.0858-0.4892-0.23570.0569-0.17690.2238-0.06080.01090.0926-0.06110.173844.02843.835-15.532
44.65880.72440.21552.80340.99082.7770.00660.3613-0.1203-0.27530.01380.05960.1912-0.1331-0.02040.0689-0.024-0.00760.0636-0.01890.05458.29275.821-13.162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 197
2X-RAY DIFFRACTION1A910
3X-RAY DIFFRACTION2B0 - 196
4X-RAY DIFFRACTION2B910
5X-RAY DIFFRACTION3C0 - 196
6X-RAY DIFFRACTION3C910
7X-RAY DIFFRACTION4D0 - 197
8X-RAY DIFFRACTION4D910

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