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- PDB-5wop: High Resolution Structure of Mutant CA09-PB2cap -

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Basic information

Entry
Database: PDB / ID: 5wop
TitleHigh Resolution Structure of Mutant CA09-PB2cap
ComponentsPolymerase PB2
KeywordsTRANSCRIPTION / Polymerase Basic Protein 2 / Cap-Snatching / RNA Polymerase / Influenza / Cap-Binding Domain / Structural Genomics
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / virion component / host cell nucleus
Similarity search - Function
: / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsConstantinides, A.E. / Gumpper, R.H. / Severin, C. / Luo, M.
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: High-resolution structure of the Influenza A virus PB2cap binding domain illuminates the changes induced by ligand binding.
Authors: Constantinides, A. / Gumpper, R. / Severin, C. / Luo, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The cap-binding site of influenza virus protein PB2 as a drug target
Authors: Severin, C. / Rocha de Moura, T. / Liu, Y. / Li, K. / Zheng, X. / Luo, M.
#2: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Crystallization and X-ray crystallographic analysis of the cap-binding domain of influenza A virus H1N1 polymerase subunit PB2
Authors: Liu, Y. / Meng, G. / Luo, M. / Zheng, X.
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Revision 1.2Oct 4, 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
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 PB2
B: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0446
Polymers35,6752
Non-polymers3684
Water6,053336
1
A: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1144
Polymers17,8381
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9302
Polymers17,8381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.863, 72.429, 61.316
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polymerase PB2 / Mutant CA09-PB2cap


Mass: 17837.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PB2 / Production host: Escherichia coli (E. coli) / References: UniProt: F4MEU3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.24 Å3/Da / Density % sol: 45.21 % / Description: Prism
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.86
Details: 0.1 M ammonium acetate, 0.1 M Bis Tris, pH 5.86, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2017
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→72.43 Å / Num. obs: 47950 / % possible obs: 99.3 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.042 / Rrim(I) all: 0.076 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.52-1.553.20.6310.8090.4250.763100
8.33-72.4330.0260.9990.0180.03194.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.15data scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EG7

5eg7


Resolution: 1.52→39 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.059 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2438 5.1 %RANDOM
Rwork0.1478 ---
obs0.1511 45487 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.43 Å2 / Biso mean: 21.183 Å2 / Biso min: 2.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.05 Å2
2---0.97 Å2-0 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 1.52→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 48 336 2873
Biso mean--86.39 31.54 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192543
X-RAY DIFFRACTIONr_bond_other_d0.0130.022475
X-RAY DIFFRACTIONr_angle_refined_deg2.2391.9663396
X-RAY DIFFRACTIONr_angle_other_deg1.19735721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25523.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.915493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3021524
X-RAY DIFFRACTIONr_chiral_restr0.1550.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022768
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_rigid_bond_restr4.13735015
X-RAY DIFFRACTIONr_sphericity_free26.6635219
X-RAY DIFFRACTIONr_sphericity_bonded13.34455102
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 194 -
Rwork0.273 3369 -
all-3563 -
obs--99.97 %
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)
10.0576-0.01430.00790.190.00090.0012-0.00140.00460.00090.00130.0013-0.01120.0001-0.00040.00010.00530.00070.00610.01180.00040.015-6.37050.164628.4877
20.0463-0.04460.01230.2194-0.00880.0037-0.00130.0037-0.00160.00450.0031-0.00710.00020.0015-0.00180.00510.00040.00510.0128-0.00040.0150.57121.9374-1.4207
30.001-0.0033-0.00040.027-0.00130.00370.00060.0018-0.00130.0026-0.0030.00150.00060.00140.00240.00480.00030.00280.0128-0.00010.0224-5.24330.88616.742
41.9906-2.00732.38462.6286-2.06753.09610.17280.42260.10050.0172-0.2333-0.07990.20390.65870.06050.33750.0150.26520.19620.00410.3925-5.7071-2.593513.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A321 - 761
2X-RAY DIFFRACTION2B4 - 479
3X-RAY DIFFRACTION3C1 - 276
4X-RAY DIFFRACTION4D1 - 6

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