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- PDB-3hw4: Crystal structure of avian influenza A virus in complex with TMP -

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Basic information

Entry
Database: PDB / ID: 3hw4
TitleCrystal structure of avian influenza A virus in complex with TMP
ComponentsPolymerase acidic protein
KeywordsHYDROLASE / avian influenza virus / PA_N / TMP / Phosphoprotein
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: 1.9 Å
AuthorsZhao, C. / Lou, Z. / Guo, Y. / Ma, M. / Chen, Y. / Rao, Z.
CitationJournal: J.Virol. / Year: 2009
Title: Nucleoside monophosphate complex structures of the endonuclease domain from the influenza virus polymerase PA subunit reveal the substrate binding site inside the catalytic center
Authors: Zhao, C. / Lou, Z. / Guo, Y. / Ma, M. / Chen, Y. / Liang, S. / Zhang, L. / Chen, S. / Li, X. / Liu, Y. / Bartlam, M. / Rao, Z.
History
DepositionJun 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
B: Polymerase acidic protein
C: Polymerase acidic protein
D: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,36111
Polymers121,2974
Non-polymers1,0647
Water7,386410
1
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6713
Polymers30,3241
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6713
Polymers30,3241
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3492
Polymers30,3241
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6713
Polymers30,3241
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.323, 60.033, 67.114
Angle α, β, γ (deg.)96.12, 96.36, 109.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 30324.307 Da / Num. of mol.: 4 / Fragment: residues in UNP 1- 256 / Mutation: V201I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Goose/Guangdong/1/96(H5N1))
Gene: PA / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Q0U9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS BELIEVE THAT ILE 201 IS CORRECT AND IT IS NATURAL MUTANT.

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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: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17.5% PEG3350 (w/v), 100mM MgAc, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 26, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 54857 / % possible obs: 95 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.264 / Num. unique all: 6789 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ebj

3ebj


Resolution: 1.9→47.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.2 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2794 5.1 %RANDOM
Rwork0.21288 ---
obs0.21617 52062 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.844 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å22.72 Å21.9 Å2
2--0.29 Å21.55 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 67 410 6359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226068
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.9568151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3923.173312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.264151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1271556
X-RAY DIFFRACTIONr_chiral_restr0.160.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024546
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_it1.3231.53534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34925722
X-RAY DIFFRACTIONr_scbond_it3.79832534
X-RAY DIFFRACTIONr_scangle_it5.9454.52429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 150 -
Rwork0.235 2744 -
obs--67.3 %

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