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- PDB-5wx1: The closed-conformation crystal structure of the full-length pest... -

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Basic information

Entry
Database: PDB / ID: 5wx1
TitleThe closed-conformation crystal structure of the full-length pestivirus NS3 with its NS4A protease cofactor segment
ComponentsSerine protease NS3
KeywordsHYDROLASE / protease / RNA helicase
Function / homology
Function and homology information


serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / protein complex oligomerization / monoatomic ion channel activity / 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 / protein complex oligomerization / monoatomic ion channel activity / 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 entry into host cell / induction by virus of host autophagy / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
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: 2.35 Å
AuthorsZheng, F. / Lu, G. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology2013CB911100 China
National Natural Science Foundation31670154 China
Ministry of Science and Technology2016YFC1200400 China
CitationJournal: J. Virol. / Year: 2017
Title: Uncoupling of Protease trans-Cleavage and Helicase Activities in Pestivirus NS3.
Authors: Zheng, F. / Lu, G. / Li, L. / Gong, P. / Pan, Z.
History
DepositionJan 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
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

Downloads & links

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Assembly

Deposited unit
A: Serine protease NS3


Theoretical massNumber of molelcules
Total (without water)81,5371
Polymers81,5371
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30720 Å2
Unit cell
Length a, b, c (Å)111.084, 111.084, 139.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Serine protease NS3 / Non-structural protein 3


Mass: 81537.039 Da / Num. of mol.: 1 / Mutation: S163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-(DE3) / References: UniProt: Q5U8X5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7 / Details: malic acid

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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: Jan 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.35→60 Å / Num. obs: 35913 / % possible obs: 97.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 41.02 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Χ2: 1.005 / Net I/σ(I): 11.4 / Num. measured all: 219021
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.436.10.51635760.8590.2220.5631.15398.5
2.43-2.536.10.43435710.9010.1870.4751.16998.3
2.53-2.656.10.31735710.9410.1360.3461.1598.3
2.65-2.796.20.22635600.9680.0970.2471.297.9
2.79-2.966.20.15835720.9860.0670.1731.10997.7
2.96-3.196.10.10835640.9920.0460.1181.04597.5
3.19-3.516.10.07735720.9950.0330.0840.84797.2
3.51-4.026.10.0835880.9940.0340.0870.85696.7
4.02-5.0660.0736160.9940.030.0770.71695.9
5.06-605.90.04737230.9960.0210.0520.893.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBG,1CU1

4cbg

1cu1


Resolution: 2.35→49.678 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1793 5 %
Rwork0.1955 34091 -
obs0.1983 35884 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.42 Å2 / Biso mean: 53.1752 Å2 / Biso min: 16.04 Å2
Refinement stepCycle: final / Resolution: 2.35→49.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 0 226 5552
Biso mean---49.14 -
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085428
X-RAY DIFFRACTIONf_angle_d1.017357
X-RAY DIFFRACTIONf_chiral_restr0.065834
X-RAY DIFFRACTIONf_plane_restr0.006954
X-RAY DIFFRACTIONf_dihedral_angle_d20.0653289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3502-2.41370.30361220.25652648277099
2.4137-2.48470.28671410.25072581272298
2.4847-2.56490.35351200.24382623274398
2.5649-2.65660.28241340.23612616275098
2.6566-2.7630.31531430.23562598274198
2.763-2.88870.32091360.22932597273398
2.8887-3.0410.29261560.22712585274198
3.041-3.23150.28321510.22712612276397
3.2315-3.48090.27671410.20312609275097
3.4809-3.83110.22811440.17792607275197
3.8311-4.38520.20991400.15722622276296
4.3852-5.52370.19831340.1532640277496
5.5237-49.68940.21541310.18962753288494
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)
10.9332-0.0231-0.02691.069-0.19630.99750.1776-0.0680.2058-0.035-0.07330.1348-0.18040.09040.00440.24340.02040.06190.1617-0.01880.2351137.754899.971356.4822
20.53240.16130.21350.7123-0.05581.119-0.03730.395-0.1567-0.18730.0470.10110.12930.37120.00030.38490.0547-0.01790.4708-0.05980.2205131.585576.579220.7466
30.98710.63760.2641.7286-0.09880.8522-0.250.0053-0.1333-0.27370.28290.2329-0.1467-0.02150.00210.2801-0.0731-0.05640.1733-0.00320.236103.727695.823328.9651
40.74020.15380.15850.8405-0.69821.0990.0841-0.0637-0.1785-0.23310.05370.14140.30510.01320.00020.28220.0024-0.08960.1472-0.01710.2577118.588972.314748.9372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -38 through 199 )A-38 - 199
2X-RAY DIFFRACTION2chain 'A' and (resid 208 through 350 )A208 - 350
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 475 or resid 490 through 525 )A364 - 475
4X-RAY DIFFRACTION3chain 'A' and (resid 364 through 475 or resid 490 through 525 )A490 - 525
5X-RAY DIFFRACTION4chain 'A' and (resid 476 through 489 or resid 526 through 683 )A476 - 489
6X-RAY DIFFRACTION4chain 'A' and (resid 476 through 489 or resid 526 through 683 )A526 - 683

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