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- PDB-3hw3: The crystal structure of avian influenza virus PA_N in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3hw3
TitleThe crystal structure of avian influenza virus PA_N in complex with UMP
ComponentsPolymerase acidic protein
KeywordsHYDROLASE / avian influenza virus / PA_N / UMP / 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 / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
URIDINE-5'-MONOPHOSPHATE / 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 1.0Oct 13, 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)121,7199
Polymers121,2974
Non-polymers4215
Water8,521473
1
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6733
Polymers30,3241
Non-polymers3482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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
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)30,3492
Polymers30,3241
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.132, 59.695, 66.850
Angle α, β, γ (deg.)96.28, 96.65, 109.44
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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 1.555854 Å3/Da / Density % sol: 20.943727 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17.5% PEG3350(w/v), 100mM MgAc, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING 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 20, 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: 54981 / % possible obs: 99 % / Observed criterion σ(F): 0 / Rsym value: 0.062
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.251 / Num. unique all: 7356 / % possible all: 95

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBJ

3ebj


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.232 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27593 2806 5.1 %RANDOM
Rwork0.21757 ---
obs0.22056 52165 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.867 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å22.13 Å21.35 Å2
2--1.84 Å20.83 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 25 473 6372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9498071
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88723.161310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.928151131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2481556
X-RAY DIFFRACTIONr_chiral_restr0.1310.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024512
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.22975
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2421
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.2168
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1661.53667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88325714
X-RAY DIFFRACTIONr_scbond_it2.87832693
X-RAY DIFFRACTIONr_scangle_it4.4134.52357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 161 -
Rwork0.249 3170 -
obs--78.43 %

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