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- PDB-4h9j: Crystal structure of N-terminal protease (Npro) of classical swin... -

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Basic information

Entry
Database: PDB / ID: 4h9j
TitleCrystal structure of N-terminal protease (Npro) of classical swine fever virus.
ComponentsHog cholera virus
KeywordsHYDROLASE / npro / csfv / autoprotease / pestivirus / cysteine-protease / cysteine protease / IRF-3 antagonist / IRF-3
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 surface / host cell cytoplasm ...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 surface / 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 / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Pestivirus Npro endopeptidase C53, interaction domain / 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 Npro endopeptidase C53, interaction domain / 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 / Spermidine Synthase; Chain: A, domain 2 / 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 / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesClassical swine fever virus
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.6 Å
AuthorsGottipati, K. / Ruggli, N. / Gerber, M. / Tratschin, J.-D. / Benning, M. / Bellamy, H. / Choi, K.H.
CitationJournal: Plos Pathog. / Year: 2013
Title: The Structure of Classical Swine Fever Virus N(pro): A Novel Cysteine Autoprotease and Zinc-Binding Protein Involved in Subversion of Type I Interferon Induction.
Authors: Gottipati, K. / Ruggli, N. / Gerber, M. / Tratschin, J.D. / Benning, M. / Bellamy, H. / Choi, K.H.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hog cholera virus


Theoretical massNumber of molelcules
Total (without water)17,2891
Polymers17,2891
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.133, 65.398, 33.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hog cholera virus


Mass: 17288.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / Strain: Alfort/187 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Rosetta-DE3) / References: UniProt: Q68871
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 1.89 Å3/Da / Density % sol: 35.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG3350, 0.2 M (NH4)2SO4 and 0.1 M Hepes, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 1, 2010 / Details: multilayer
RadiationMonochromator: multilayer confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.58→29.76 Å / Num. all: 18866 / Num. obs: 18840 / % possible obs: 99.86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 34.32 % / Rsym value: 0.042 / Net I/σ(I): 12.63
Reflection shellResolution: 1.58→1.62 Å / Mean I/σ(I) obs: 1.98 / Num. unique all: 1447 / Rsym value: 0.318 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→29.685 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 18.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1664 9.26 %RANDOM
Rwork0.1709 ---
obs0.1744 17961 99.97 %-
all-17961 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→29.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 0 224 1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071155
X-RAY DIFFRACTIONf_angle_d1.1231567
X-RAY DIFFRACTIONf_dihedral_angle_d12.25432
X-RAY DIFFRACTIONf_chiral_restr0.082166
X-RAY DIFFRACTIONf_plane_restr0.005203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64710.22851340.17941319X-RAY DIFFRACTION100
1.6471-1.70020.20171260.17271334X-RAY DIFFRACTION100
1.7002-1.7610.21471510.17271355X-RAY DIFFRACTION100
1.761-1.83150.21281250.17321328X-RAY DIFFRACTION100
1.8315-1.91490.22041340.16361326X-RAY DIFFRACTION100
1.9149-2.01580.20951420.16961348X-RAY DIFFRACTION100
2.0158-2.1420.21931290.1631358X-RAY DIFFRACTION100
2.142-2.30740.18641410.16781348X-RAY DIFFRACTION100
2.3074-2.53950.2351440.17731361X-RAY DIFFRACTION100
2.5395-2.90670.19221380.1941362X-RAY DIFFRACTION100
2.9067-3.6610.20191440.16511388X-RAY DIFFRACTION100
3.661-29.69030.20851560.16571470X-RAY DIFFRACTION100

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