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- PDB-4p9a: X-ray Crystal Structure of PA protein from Influenza strain H7N9 -

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Basic information

Entry
Database: PDB / ID: 4p9a
TitleX-ray Crystal Structure of PA protein from Influenza strain H7N9
ComponentsPolymerase PA
KeywordsVIRAL PROTEIN / PA protein Influenza H7N9 polymerase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / viral RNA genome replication / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
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 acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1999 Å
AuthorsFairman, J.W. / Moen, S.O. / Clifton, M.C. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Rep / Year: 2014
Title: Structural analysis of H1N1 and H7N9 influenza A virus PA in the absence of PB1.
Authors: Moen, S.O. / Abendroth, J. / Fairman, J.W. / Baydo, R.O. / Bullen, J. / Kirkwood, J.L. / Barnes, S.R. / Raymond, A.C. / Begley, D.W. / Henkel, G. / McCormack, K. / Tam, V.C. / Phan, I. / ...Authors: Moen, S.O. / Abendroth, J. / Fairman, J.W. / Baydo, R.O. / Bullen, J. / Kirkwood, J.L. / Barnes, S.R. / Raymond, A.C. / Begley, D.W. / Henkel, G. / McCormack, K. / Tam, V.C. / Phan, I. / Staker, B.L. / Stacy, R. / Myler, P.J. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4302
Polymers53,3381
Non-polymers921
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-1 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.890, 68.890, 400.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Polymerase PA


Mass: 53338.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/chicken/Zhejiang/DTID-ZJU01/2013(H7N9) / Gene: PA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: M9V5W3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 400 nl of protein solution at 20.77 mg/ml plus 400 nl precipitant solution equilibrated against 80 uL of precipitant. Precipitant: Wizard 3/4 well A10 - 200 mM sodium thiocyanate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 20, 2014
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1999→50 Å / Num. obs: 30002 / Observed criterion σ(I): -3 / Redundancy: 5.87 % / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.063 / Χ2: 0.97 / Net I/σ(I): 19.93
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1999-2.260.810.5853.113101216121610.641100
2.26-2.320.880.4414.0112507208720870.484100
2.32-2.390.9130.3954.5812549207720770.433100
2.39-2.460.9410.3025.8911937199519940.33299.9
2.46-2.540.9740.2297.6611678193519350.251100
2.54-2.630.9750.2048.4811109186018600.224100
2.63-2.730.9830.16810.0910987182818280.184100
2.73-2.840.9910.1312.4610498175517550.143100
2.84-2.970.9940.09716.539999167916790.106100
2.97-3.110.9960.07720.149703163016300.084100
3.11-3.280.9970.06323.839201155815580.07100
3.28-3.480.9980.0529.68569146014590.05599.9
3.48-3.720.9980.0436.778112139313930.044100
3.72-4.020.9990.03640.217547131813170.0499.9
4.02-4.40.9990.03145.236905120912050.03599.7
4.4-4.920.9990.0346.636239112311220.03399.9
4.92-5.680.9990.02945.6355539949940.032100
5.68-6.960.9990.02844.0846418718590.03298.6
6.96-9.840.9990.02451.1736057016900.02698.4
9.84-500.9990.02251.0217994403990.02590.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZNL

2znl


Resolution: 2.1999→35.653 Å / FOM work R set: 0.851 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1466 4.89 %Random
Rwork0.2027 28528 --
obs0.204 29994 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.67 Å2 / Biso mean: 58.06 Å2 / Biso min: 27.04 Å2
Refinement stepCycle: final / Resolution: 2.1999→35.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 6 92 3010
Biso mean--91.58 48.51 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083018
X-RAY DIFFRACTIONf_angle_d0.9754099
X-RAY DIFFRACTIONf_chiral_restr0.038467
X-RAY DIFFRACTIONf_plane_restr0.004520
X-RAY DIFFRACTIONf_dihedral_angle_d12.841091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1999-2.27850.24711500.215227652915100
2.2785-2.36980.23891410.21327872928100
2.3698-2.47760.23931420.212327822924100
2.4776-2.60820.25171310.209527822913100
2.6082-2.77150.27151340.222528352969100
2.7715-2.98540.22861220.230128582980100
2.9854-3.28570.26991580.218628172975100
3.2857-3.76070.19881580.189228683026100
3.7607-4.73630.20661710.172729013072100
4.7363-35.65720.22981590.21023133329298
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)
11.93811.3999-1.55662.05110.19993.16870.1788-0.21970.2331-0.04-0.2392-0.1477-0.1923-0.0104-0.06760.18830.04350.03690.6180.07590.303618.757431.361214.2697
23.5630.6467-0.7131.83421.05563.69610.00030.38170.4355-0.0842-0.12140.2042-0.39590.07470.01130.2227-0.03760.02120.64610.1390.377526.17939.19570.3221
31.39670.09251.20831.7742-0.24433.2454-0.2467-0.0147-0.56420.4093-0.2022-0.18690.53940.77350.23930.28410.03560.01050.75140.14610.430223.990321.30319.6796
42.45230.283-0.20531.79280.08973.47340.0507-0.1782-0.09020.233-0.00810.182-0.1073-0.3345-0.03910.19460.05860.0290.58170.1150.328413.009630.61813.1837
51.72490.35690.70673.7841-1.87681.3816-0.09110.0176-0.48190.5539-0.30470.67340.5877-0.71110.20040.5592-0.18460.17160.7370.09070.5258.191614.405826.8262
62.03021.3767-0.84433.828-3.82694.3561-0.17070.0801-0.7616-0.2557-0.5391-0.68781.11020.05890.64770.6348-0.00540.18680.7230.20970.574719.2334.942326.9213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 313 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 314 through 369 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 415 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 416 through 596 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 597 through 671 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 672 through 713 )A0

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