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- PDB-4cbl: Pestivirus NS3 helicase -

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Basic information

Entry
Database: PDB / ID: 4cbl
TitlePestivirus NS3 helicase
ComponentsSERINE PROTEASE NS3
KeywordsHYDROLASE / SF2 HELICASES / PESTIVIRUS / FLAVIVIRIDAE NS3 / SAXS
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / 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 / entry receptor-mediated virion attachment to host cell ...pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / 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 / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / viral protein processing / RNA helicase / symbiont entry into host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / GTP binding / host cell plasma membrane / virion membrane / ATP hydrolysis activity / 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 / P-loop containing nucleotide triphosphate hydrolases / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCLASSICAL SWINE FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsTortorici, M.A. / Duquerroy, S. / Kwok, J. / Vonrhein, C. / Perez, J. / Lamp, B. / Bricogne, G. / Rumenapf, T. / Vachette, P. / Rey, F.A.
CitationJournal: J.Virol. / Year: 2015
Title: X-Ray Structure of the Pestivirus Ns3 Helicase and its Conformation in Solution.
Authors: Tortorici, M.A. / Duquerroy, S. / Kwok, J. / Vonrhein, C. / Perez, J. / Lamp, B. / Bricogne, G. / Rumenapf, T. / Vachette, P. / Rey, F.A.
History
DepositionOct 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SERINE PROTEASE NS3
B: SERINE PROTEASE NS3
C: SERINE PROTEASE NS3
D: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)228,8814
Polymers228,8814
Non-polymers00
Water00
1
A: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)57,2201
Polymers57,2201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)57,2201
Polymers57,2201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)57,2201
Polymers57,2201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)57,2201
Polymers57,2201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.910, 156.840, 99.400
Angle α, β, γ (deg.)90.00, 97.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.8409, 0.4903, 0.2292), (0.4898, -0.8695, 0.06334), (0.2303, 0.05899, -0.9713)-78.54, 186.8, 231.3
3given(-0.9998, 0.000567, 0.02068), (-0.01898, -0.4225, -0.9062), (0.008224, -0.9064, 0.4224)-9.794, 253.4, 159.6
4given(-0.8249, -0.4552, -0.3352), (-0.5004, 0.3122, 0.8075), (-0.2629, 0.8339, -0.4853)78.53, -23.58, 88.67

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Components

#1: Protein
SERINE PROTEASE NS3 / NON-STRUCTURAL PROTEIN 3


Mass: 57220.191 Da / Num. of mol.: 4 / Fragment: HELICASE DOMAIN, 1792-2280 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLASSICAL SWINE FEVER VIRUS / Strain: ALFORT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P19712, pestivirus NS3 polyprotein peptidase, nucleoside-triphosphate phosphatase, RNA helicase

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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: 2.41 Å3/Da / Density % sol: 49.02 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M NA-CACODYLATE, 0.15 M CALCIUM ACETATE, 12% PEG 3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→39.21 Å / Num. obs: 38441 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 75.82 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.8 / % possible all: 73.3

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CBG

4cbg


Resolution: 3.05→20 Å / Cor.coef. Fo:Fc: 0.9039 / Cor.coef. Fo:Fc free: 0.8656 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.417
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1915 5 %RANDOM
Rwork0.1944 ---
obs0.1959 38280 94.88 %-
Displacement parametersBiso mean: 82.64 Å2
Baniso -1Baniso -2Baniso -3
1-12.6529 Å20 Å22.3807 Å2
2---29.8146 Å20 Å2
3---17.1617 Å2
Refine analyzeLuzzati coordinate error obs: 0.559 Å
Refinement stepCycle: LAST / Resolution: 3.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14954 0 0 0 14954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1420595HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5380SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes395HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2175HARMONIC5
X-RAY DIFFRACTIONt_it15220HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion21.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1986SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17854SEMIHARMONIC4
LS refinement shellResolution: 3.05→3.13 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2777 117 5.46 %
Rwork0.2488 2027 -
all0.2502 2144 -
obs--94.88 %

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