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- PDB-4cbm: Pestivirus NS3 helicase -

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Basic information

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


pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / channel activity / monoatomic ion transmembrane transport / 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-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / 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 / Reverse transcriptase/Diguanylate cyclase domain / P-loop containing nucleotide triphosphate hydrolases / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCLASSICAL SWINE FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 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 4, 2015Group: Atomic model / Derived calculations / Other
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Dec 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

Downloads & links

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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)232,0964
Polymers232,0964
Non-polymers00
Water181
1
A: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0241
Polymers58,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0241
Polymers58,0241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0241
Polymers58,0241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0241
Polymers58,0241
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.100, 159.585, 99.227
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.8308, -0.4508, -0.3264), (-0.4816, 0.2882, 0.8277), (-0.279, 0.8448, -0.4565)-47.53, -121.2, 164.6
3given(0.8126, 0.5429, 0.2122), (0.5469, -0.836, 0.04444), (0.2015, 0.07995, -0.9762)78.68, -284.5, 53.36
4given(-0.9979, -0.02748, 0.05796), (-0.03932, -0.4518, -0.8912), (0.05068, -0.8917, 0.4498)10.23, -202.7, -126.3

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Components

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


Mass: 58024.086 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.46 Å3/Da / Density % sol: 49.93 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1 M NAAC, 0.025 M CALCIUM ACETATE, 9 % PEG 4000, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 3.27→37.98 Å / Num. obs: 31533 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 59.76 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7
Reflection shellResolution: 3.27→3.45 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.9 / % possible all: 91.7

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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: 3.27→20 Å / Cor.coef. Fo:Fc: 0.7419 / Cor.coef. Fo:Fc free: 0.6606 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.613
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 1585 5.05 %RANDOM
Rwork0.233 ---
obs0.2355 31359 94.05 %-
Displacement parametersBiso mean: 64.53 Å2
Baniso -1Baniso -2Baniso -3
1-21.0748 Å20 Å24.4206 Å2
2---56.5045 Å20 Å2
3---35.4297 Å2
Refine analyzeLuzzati coordinate error obs: 0.688 Å
Refinement stepCycle: LAST / Resolution: 3.27→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14615 0 0 1 14616
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114892HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1520130HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5300SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes387HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2113HARMONIC5
X-RAY DIFFRACTIONt_it14892HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion22.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1942SEMIHARMONIC5
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_contact17575SEMIHARMONIC4
LS refinement shellResolution: 3.27→3.38 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3617 148 5.31 %
Rwork0.2842 2637 -
all0.288 2785 -
obs--94.05 %

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