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- PDB-3kc6: Crystal structure of the large c-terminal domain of polymerase ba... -

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Basic information

Entry
Database: PDB / ID: 3kc6
TitleCrystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)
ComponentsPolymerase PB2
KeywordsVIRAL PROTEIN / Bird flu / structural genomics / NIAID / mRNA capping / mRNA processing / 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 / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain ...Polymerase Basic Protein 2, C-terminal domain / Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / : / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 6th domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos Pathog. / Year: 2010
Title: Biological and structural characterization of a host-adapting amino acid in influenza virus.
Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. ...Authors: Yamada, S. / Hatta, M. / Staker, B.L. / Watanabe, S. / Imai, M. / Shinya, K. / Sakai-Tagawa, Y. / Ito, M. / Ozawa, M. / Watanabe, T. / Sakabe, S. / Li, C. / Kim, J.H. / Myler, P.J. / Phan, I. / Raymond, A. / Smith, E. / Stacy, R. / Nidom, C.A. / Lank, S.M. / Wiseman, R.W. / Bimber, B.N. / O'Connor, D.H. / Neumann, G. / Stewart, L.J. / Kawaoka, Y.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3May 23, 2012Group: Database references
Revision 1.4Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Polymerase PB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9514
Polymers22,7651
Non-polymers1863
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.084, 65.696, 96.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsUNKNOWN

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Components

#1: Protein Polymerase PB2 / Polymerase basic subunit 2 / Polymerase protein PB2


Mass: 22765.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Strain: A/VIET NAM/1203/2004 (H5N1) / Gene: PB2 / Plasmid: PET28-SMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6DNN3
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 5% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, ...Details: 5% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 31, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 13728 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 4 % / Rmerge(I) obs: 0.328 / % possible all: 88.5

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0104refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CW4

3cw4


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.239 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.245 684 5 %RANDOM
Rwork0.202 ---
obs0.204 13682 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---1.01 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 12 92 1607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221540
X-RAY DIFFRACTIONr_bond_other_d0.0010.021040
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9662084
X-RAY DIFFRACTIONr_angle_other_deg0.83432538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8224.53164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74615251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.226159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5821.5982
X-RAY DIFFRACTIONr_mcbond_other0.1061.5401
X-RAY DIFFRACTIONr_mcangle_it1.05421572
X-RAY DIFFRACTIONr_scbond_it1.4533558
X-RAY DIFFRACTIONr_scangle_it2.3964.5512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 54 -
Rwork0.204 855 -
obs--91.08 %
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)
10.7838-0.07230.23553.366-0.46380.5261-0.03240.00080.0354-0.20040.0758-0.0197-0.00710.0594-0.04350.1225-0.0061-0.00170.1342-0.00420.1262.64.727-23.273
21.6428-1.8950.63555.61960.03321.28290.00510.1152-0.17020.1930.06070.52530.1483-0.0515-0.06590.0744-0.02060.0020.12550.02430.1917-5.573-2.836-19.035
30.53880.2776-0.53114.2070.69440.72210.0118-0.1009-0.15360.29940.0799-0.2602-0.04240.059-0.09170.13330.0359-0.03790.14250.00540.13343.938-2.83-14.215
44.55980.9129-2.26076.6891-1.46786.20270.0536-0.2953-0.13360.2848-0.03360.2017-0.2196-0.3007-0.02010.21120.09430.06240.17130.02620.0126-9.6773.47-0.253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A540 - 626
2X-RAY DIFFRACTION2A627 - 663
3X-RAY DIFFRACTION3A664 - 696
4X-RAY DIFFRACTION4A697 - 739

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