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- PDB-4iuj: Structure of Polymerase acid protein (PA) from Influenzavirus A I... -

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Basic information

Entry
Database: PDB / ID: 4iuj
TitleStructure of Polymerase acid protein (PA) from Influenzavirus A Influenza A virus A, WILSON-SMITH/1933 (H1N1)
ComponentsPolymerase acidic protein
KeywordsTRANSCRIPTION / SSGCID / Influenza / H1N1 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / host cell cytoplasm / Hydrolases; Acting on ester bonds ...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 / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
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
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein


Theoretical massNumber of molelcules
Total (without water)53,0971
Polymers53,0971
Non-polymers00
Water4,594255
1
A: Polymerase acidic protein

A: Polymerase acidic protein


Theoretical massNumber of molelcules
Total (without water)106,1932
Polymers106,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3360 Å2
ΔGint-10 kcal/mol
Surface area36050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.800, 68.800, 395.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-946-

HOH

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Components

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


Mass: 53096.723 Da / Num. of mol.: 1 / Fragment: UNP residues 254-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Wilson-Smith/1933(H1N1) / Gene: PA / Plasmid: InvaN.07057.a.D15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15659
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.55 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen g50: 10% PEG 8000, 20% ethylene glycol; 20mM of each Na-formate, Ammonium-acetate, Na3-citrate, NaK D/L tartrate, Na-oxamate; 100mM MOPS/HEPES pH 7.5; ...Details: Molecular Dimensions Morpheus screen g50: 10% PEG 8000, 20% ethylene glycol; 20mM of each Na-formate, Ammonium-acetate, Na3-citrate, NaK D/L tartrate, Na-oxamate; 100mM MOPS/HEPES pH 7.5; INVAN.07057.A.D15.PD909136 AT 20.45MG/ML, direct cryo, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2012
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 45568 / Num. obs: 45117 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 35.36 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.950.524.542947332631100
1.95-20.3915.812880331791100
2-2.060.3037.31281933120199.9
2.06-2.120.2458.86274553025199.8
2.12-2.190.18311.36264262923199.8
2.19-2.270.15213.36256012831199.8
2.27-2.360.12715.51248992757199.7
2.36-2.450.11316.95241512667199.7
2.45-2.560.09519.8229872541199.5
2.56-2.690.08721.28218112437199.4
2.69-2.830.07723.8209832334199.3
2.83-30.06827.69198722214199.1
3-3.210.06230.1183632067198.8
3.21-3.470.05932.41173291965198.6
3.47-3.80.05634.88158361809198.4
3.8-4.250.05535.94143181649198
4.25-4.910.05336.29126371475197.4
4.91-6.010.05335.14105161254196.5
6.01-8.50.05434.7882581021195.8
8.5-500.05232.093943586184.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.86 Å
Translation3.5 Å19.86 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2znl

2znl


Resolution: 1.9→47.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2071 / WRfactor Rwork: 0.1795 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.898 / SU B: 4.784 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1169 / SU Rfree: 0.1113 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2279 5.1 %RANDOM
Rwork0.1737 ---
all0.1751 45568 --
obs0.1751 45103 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.82 Å2 / Biso mean: 37.196 Å2 / Biso min: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.05 Å20 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 0 255 3450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193301
X-RAY DIFFRACTIONr_bond_other_d0.0010.023164
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9674471
X-RAY DIFFRACTIONr_angle_other_deg0.76337296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.51724.286140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19915599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
X-RAY DIFFRACTIONr_mcbond_it1.3742.0681642
X-RAY DIFFRACTIONr_mcbond_other1.3732.0661641
X-RAY DIFFRACTIONr_mcangle_it2.1643.0822049
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 169 -
Rwork0.212 3084 -
all-3253 -
obs--100 %
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)
10.4487-0.2864-0.05670.9767-0.24611.1997-0.03680.0315-0.0018-0.04030.0225-0.0068-0.0632-0.10410.01430.15050.11210.01650.10420.01970.036-19.09-27.62551.829
22.61181.6224-1.22743.822-0.25033.1684-0.1511-0.0938-0.0254-0.1159-0.0765-0.6588-0.56240.58950.22760.2228-0.0885-0.02130.22030.13710.25144.292-17.76339.627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A266 - 652
2X-RAY DIFFRACTION2A653 - 713

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