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- PDB-4cbi: Pestivirus NS3 helicase -

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Basic information

Entry
Database: PDB / ID: 4cbi
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 ...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 / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / 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 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 1.4Oct 14, 2015Group: Refinement description
Revision 1.5Dec 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)232,0924
Polymers232,0924
Non-polymers00
Water30617
1
A: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.633, 96.303, 97.611
Angle α, β, γ (deg.)91.23, 110.86, 107.62
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.8215, 0.4069, -0.3995), (-0.4421, -0.01204, 0.8969), (0.3601, 0.9134, 0.1898)5.337, -55.22, 54.59
3given(0.3488, 0.7242, -0.595), (0.7274, -0.6094, -0.3153), (-0.5909, -0.3228, -0.7393)28.73, 45.13, 120.5
4given(-0.8209, -0.4213, 0.3856), (-0.4398, 0.03556, -0.8974), (0.3644, -0.9062, -0.2145)-41.12, 65.1, 95.97

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Components

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


Mass: 58023.031 Da / Num. of mol.: 4 / Fragment: HELICASE DOMAIN, RESIDUES 1782-2280
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 / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHISTAG N-TERMINAL PLUS TEV CLEAVAGE SITE

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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: 2.92 Å3/Da / Density % sol: 57.87 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES, 0.6 M NACL, 4% PEG, 1 MM AMPPCP, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→46.83 Å / Num. obs: 40172 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 65.06 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.7 / % possible all: 68.4

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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→15 Å / Cor.coef. Fo:Fc: 0.9033 / Cor.coef. Fo:Fc free: 0.8759 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.418
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1980 4.97 %RANDOM
Rwork0.2098 ---
obs0.2115 39850 89.79 %-
Displacement parametersBiso mean: 89.64 Å2
Baniso -1Baniso -2Baniso -3
1-6.1962 Å2-2.8447 Å21.6314 Å2
2---18.0852 Å29.7855 Å2
3---11.8891 Å2
Refine analyzeLuzzati coordinate error obs: 0.504 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13710 0 0 17 13727
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114033HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1218963HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4982SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes363HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1984HARMONIC5
X-RAY DIFFRACTIONt_it14033HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion22.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1842SEMIHARMONIC5
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_contact16492SEMIHARMONIC4
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2594 97 4.68 %
Rwork0.2321 1977 -
all0.2334 2074 -
obs--89.79 %
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)
13.5220.88010.55083.1481.32034.4112-0.01030.4098-0.07810.0969-0.0530.22570.3714-0.13750.0633-0.3762-0.0237-0.02630.22160.0146-0.0198-26.950113.006640.2007
24.46190.5271-0.49923.5721-0.13281.4559-0.24060.1074-0.1422-0.6010.2117-0.49330.5424-0.3140.0289-0.0609-0.18150.1985-0.04650.0025-0.1253-1.1676-8.679327.0178
35.1721-0.6443-1.06251.18240.29973.3005-0.02780.05490.29740.09480.072-0.2508-0.20880.2966-0.0442-0.3591-0.0665-0.03610.334-0.07430.153.850420.920943.0155
44.2416-1.9378-1.27515.15181.64163.237-0.23180.4455-0.6829-0.30780.1364-0.01770.35270.270.0954-0.2555-0.0844-0.0038-0.1735-0.14380.1171-9.1089-27.560471.4004
54.34021.9496-1.01852.80372.25674.9347-0.1605-0.2194-0.6776-0.27340.0668-0.30230.4469-0.24230.09370.0686-0.2739-0.03930.14630.0857-0.2464-23.8117-26.986640.564
67.26110.94472.30550.87590.69463.0772-0.03870.5344-0.1504-0.3217-0.12550.4019-0.0736-0.43910.1642-0.2433-0.099-0.15520.2957-0.00010.1028-36.579-11.698666.8015
74.1075-0.8488-0.94383.74191.29664.67650.045-0.33520.2449-0.1129-0.16650.2885-0.32-0.34310.1215-0.3322-0.1007-0.01950.30420.03910.1203-26.9562.686494.4889
82.94120.29030.80633.23021.5934.958-0.37920.16920.27860.62440.2186-0.2255-0.6864-0.13340.1607-0.16510.1225-0.2021-0.09550.0574-0.1568-1.60323.6522108.036
95.61531.09871.22462.26430.02312.80890.0219-0.1622-0.2149-0.04540.0409-0.26420.19620.4075-0.0628-0.42070.01570.03060.2082-0.0733-0.04223.8815-5.081491.4612
103.8366-0.1986-0.42042.65472.5673.4152-0.0824-0.36880.73350.18280.3097-0.234-0.48980.3743-0.2273-0.3001-0.0647-0.014-0.1535-0.190.2463-9.138843.436762.8783
115.6521-1.02582.7699-1.2337-0.11377.2605-0.45510.15640.40240.59710.0425-0.0831-0.1747-0.11570.41260.17510.2576-0.0234-0.01280.0224-0.0847-24.221638.856193.6492
124.8752-1.0698-1.922.54241.37535.1004-0.1993-0.36350.21740.3645-0.1330.59060.0731-0.63080.3323-0.446-0.00560.08790.1566-0.0648-0.084-37.115328.057667.8042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|206 - A|353}
2X-RAY DIFFRACTION2{A|364 - A|476,A|489 - A|522}
3X-RAY DIFFRACTION3{A|477 - A|488,A|526 - A|684}
4X-RAY DIFFRACTION4{B|206 - B|351}
5X-RAY DIFFRACTION5{B|364 - B|476,B|489 - B|525}
6X-RAY DIFFRACTION6{B|477 - B|488,B|526 - B|683}
7X-RAY DIFFRACTION7{C|205 - C|353}
8X-RAY DIFFRACTION8{C|364 - C|476,C|489 - C|520}
9X-RAY DIFFRACTION9{C|477 - C|488,C|525 - C|686}
10X-RAY DIFFRACTION10{D|206 - D|350}
11X-RAY DIFFRACTION11{ D|368 - D|476,D|489 - D|525}
12X-RAY DIFFRACTION12{D|477 - D|488,D|526 - D|681}

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