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- PDB-5yf5: Crystals structure of Classical swine fever virus NS5B (residues ... -

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Basic information

Entry
Database: PDB / ID: 5yf5
TitleCrystals structure of Classical swine fever virus NS5B (residues 1-694)
ComponentsRdRp catalytic
KeywordsTRANSFERASE
Function / homology
Function and homology information


serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / 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 / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / 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 / symbiont entry into host cell / 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: 2.49 Å
AuthorsLiu, W. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670154 China
National Key Basic Research Program of China2013CB911100 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
DepositionSep 20, 2017Deposition 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)80,8211
Polymers80,8211
Non-polymers00
Water1,45981
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 area27660 Å2
Unit cell
Length a, b, c (Å)160.029, 160.029, 55.216
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: 80821.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / 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.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence details690 ALA is likely a naturally occurred mutation during multiple rounds of virus passage from its ...690 ALA is likely a naturally occurred mutation during multiple rounds of virus passage from its parental virus.

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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: 2.19 Å3/Da / Density % sol: 43.76 % / Mosaicity: 0.939 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8 / Details: Polypropylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.49→60 Å / Num. obs: 25700 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 46.19 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Χ2: 1.044 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.596.80.51925100.9170.2120.5621.044100
2.59-2.696.90.40925320.950.1660.4431.097100
2.69-2.8270.30925280.9710.1250.3341.076100
2.82-2.9670.2125320.9840.0850.2261.085100
2.96-3.1570.15225460.990.0620.1641.104100
3.15-3.396.90.10325460.9960.0420.1111.06299.9
3.39-3.736.80.07625700.9970.0310.0831.03799.9
3.73-4.276.50.06625930.9970.0270.0710.94299.9
4.27-5.386.30.05626050.9970.0240.0610.98599.7
5.38-606.20.04227380.9980.0180.0460.99997.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJQ

2cjq


Resolution: 2.49→32.397 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.81
RfactorNum. reflection% reflection
Rfree0.2423 1283 5.01 %
Rwork0.1853 --
obs0.1882 25631 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.35 Å2 / Biso mean: 52.2645 Å2 / Biso min: 30.01 Å2
Refinement stepCycle: final / Resolution: 2.49→32.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 0 81 5097
Biso mean---45.41 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085122
X-RAY DIFFRACTIONf_angle_d0.9186925
X-RAY DIFFRACTIONf_chiral_restr0.048769
X-RAY DIFFRACTIONf_plane_restr0.006880
X-RAY DIFFRACTIONf_dihedral_angle_d11.2173082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.58960.31051370.242726512788100
2.5896-2.70740.30311420.235326562798100
2.7074-2.85010.33171300.228426672797100
2.8501-3.02850.27791620.217226762838100
3.0285-3.26220.2981460.207426852831100
3.2622-3.59010.27211460.195826772823100
3.5901-4.10870.24811320.167927232855100
4.1087-5.17310.20621500.1532737288799
5.1731-32.39980.1781380.17242876301499

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