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- PDB-6ae5: Crystals structure of Classical swine fever virus NS5B (residues ... -

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Basic information

Entry
Database: PDB / ID: 6ae5
TitleCrystals structure of Classical swine fever virus NS5B (residues 1-672, Y471A mutant, form 1)
ComponentsRdRp catalytic
KeywordsTRANSFERASE / Polymerase
Function / homology
Function and homology information


serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / viral protein processing ...serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont entry into host cell / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / GTP binding / virion attachment to host cell / virion membrane / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 ...Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / : / Flavivirus NS3 helicase, C-terminal helical domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesClassical swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.754 Å
AuthorsLiu, W. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670154 China
Ministry of Science and Technology (China)2018YFA0507200 China
Ministry of Science and Technology (China)2018YFD0500100 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase.
Authors: Liu, W. / Shi, X. / Gong, P.
History
DepositionAug 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Nov 22, 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

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Assembly

Deposited unit
A: RdRp catalytic


Theoretical massNumber of molelcules
Total (without water)78,0641
Polymers78,0641
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27690 Å2
Unit cell
Length a, b, c (Å)160.653, 160.653, 55.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RdRp catalytic


Mass: 78064.328 Da / Num. of mol.: 1 / Mutation: Y471A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / Strain: Shimen / Gene: NS5B / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5U8X5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Polypropylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 19483 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 49.52 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.034 / Rrim(I) all: 0.123 / Χ2: 1.012 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.8512.20.45619080.9660.1360.4770.947100
2.85-2.9613.30.3719080.9770.1040.3840.983100
2.96-3.113.50.28919100.9840.0810.30.977100
3.1-3.2613.20.23419120.9890.0660.2431.009100
3.26-3.4612.50.17719220.9930.0520.1851.075100
3.46-3.73130.13919280.9940.040.1451.078100
3.73-4.1113.40.10719180.9970.030.1121.031100
4.11-4.712.40.08619710.9970.0250.0890.993100
4.7-5.9213.20.08219790.9980.0230.0851.018100
5.92-5011.60.07821270.9950.0240.0821.01399.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJQ

2cjq


Resolution: 2.754→45.743 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2326 967 4.98 %
Rwork0.1807 --
obs0.1833 19408 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.29 Å2 / Biso mean: 52.1653 Å2 / Biso min: 30.27 Å2
Refinement stepCycle: final / Resolution: 2.754→45.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5066 0 0 55 5121
Biso mean---43.99 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085176
X-RAY DIFFRACTIONf_angle_d0.8827001
X-RAY DIFFRACTIONf_chiral_restr0.051776
X-RAY DIFFRACTIONf_plane_restr0.005890
X-RAY DIFFRACTIONf_dihedral_angle_d9.6663115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7538-2.8990.29831390.22122559269899
2.899-3.08060.30061410.215725962737100
3.0806-3.31840.27861280.217125822710100
3.3184-3.65220.25781290.189326172746100
3.6522-4.18040.22031460.159526182764100
4.1804-5.26560.19721380.148926702808100
5.2656-45.74910.20391460.18412799294599

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