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- PDB-5ifc: Crystal structure of polymerase acid protein (PA) from Influenza ... -

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Basic information

Entry
Database: PDB / ID: 5ifc
TitleCrystal structure of polymerase acid protein (PA) from Influenza A virus, WILSON-SMITH/1933 (H1N1) bound to follow on fragment EBSI-4720 1-(4-bromophenyl)-1H-imidazole
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / NIAID / flu / structural genomics / fragment screening / STD NMR / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm ...RNA polymerase activity / negative regulation of viral transcription / negative stranded viral RNA replication / negative regulation of viral genome replication / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / protein import into nucleus / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / DNA-templated transcription / 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
1-(4-bromophenyl)-1H-imidazole / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Fragment screening by STD NMR identifies novel site binders against influenza A virus polymerase PA
Authors: Pierce, P. / Muruthi, M.M. / Abendroth, J. / Moen, S.O. / Begley, D.W. / Davies, D.R. / Marathias, V.M. / Staker, B.L. / Myler, P.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3983
Polymers53,0971
Non-polymers3012
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area19700 Å2
2
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7966
Polymers106,1932
Non-polymers6024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3700 Å2
ΔGint-8 kcal/mol
Surface area36240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.080, 69.080, 397.970
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 acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 53096.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Wilson-Smith/1933 H1N1)
Strain: A/Wilson-Smith/1933 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: P15659
#2: Chemical ChemComp-6AR / 1-(4-bromophenyl)-1H-imidazole


Mass: 223.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7BrN2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 mg/mL protein against Morpheus screen condition E10 with 10% PEG 8000, 20% EG, 0.02 M each ethylene glycol, 0.1 M bicine/Trizma pH 8.5, unique puck ID lum0-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.99985 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.65→41.212 Å / Num. obs: 17495 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.65-2.720.613.1199.8
2.72-2.790.5093.62199.9
2.79-2.870.394.551100
2.87-2.960.3165.571100
2.96-3.060.2626.661100
3.06-3.170.2058.24199.9
3.17-3.290.1769.53199.8
3.29-3.420.12512.31100
3.42-3.570.10115.59199.8
3.57-3.750.08517.7199.9
3.75-3.950.0720.341100
3.95-4.190.05923.6199.8
4.19-4.480.05325.611100
4.48-4.840.04627.861100
4.84-5.30.04826.511100
5.3-5.930.05323.61199.8
5.93-6.840.04925.061100
6.84-8.380.03929.53199.8
8.38-11.850.02836.35199.3
11.85-41.2120.02935.12192.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.65→41.212 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.2337 865 4.95 %
Rwork0.1778 --
obs0.1805 17492 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 143.55 Å2 / Biso mean: 48.9124 Å2 / Biso min: 20.78 Å2
Refinement stepCycle: final / Resolution: 2.65→41.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 16 73 3269
Biso mean--65.42 45.08 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083294
X-RAY DIFFRACTIONf_angle_d0.8764461
X-RAY DIFFRACTIONf_chiral_restr0.045497
X-RAY DIFFRACTIONf_plane_restr0.005568
X-RAY DIFFRACTIONf_dihedral_angle_d13.3291999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6501-2.81610.27591370.212726412778100
2.8161-3.03350.2681380.205527072845100
3.0335-3.33860.27971590.192626942853100
3.3386-3.82140.23091370.170127592896100
3.8214-4.81340.20171500.14927892939100
4.8134-41.21670.22031440.18313037318199
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)
11.06190.38560.60782.6342-0.82293.2135-0.0040.04660.375-0.1682-0.0758-0.01930.0629-0.02570.00510.34880.10680.04820.28720.09560.3258-15.5193-30.70250.2413
20.6841-0.27690.20771.6913-0.59082.5007-0.02560.07610.0857-0.04120.0647-0.006-0.1984-0.17150.0040.30890.1240.06440.2690.05270.2873-19.4141-27.314252.3737
32.54750.8183-2.51130.326-0.67442.7413-0.1467-0.14150.2445-0.4022-0.2595-0.7209-0.49470.76060.21140.5864-0.07730.05820.56250.26440.66664.5884-17.531639.2701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 302 )A266 - 302
2X-RAY DIFFRACTION2chain 'A' and (resid 303 through 652 )A303 - 652
3X-RAY DIFFRACTION3chain 'A' and (resid 653 through 713 )A653 - 713

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