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- PDB-4cbg: Pestivirus NS3 helicase -

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Basic information

Entry
Database: PDB / ID: 4cbg
TitlePestivirus NS3 helicase
ComponentsSERINE PROTEASE NS3
KeywordsHYDROLASE / 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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesCLASSICAL SWINE FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.82 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 ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Oct 14, 2015Group: Refinement description
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,1496
Polymers236,0314
Non-polymers1182
Water2,198122
1
A: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)59,0081
Polymers59,0081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)59,0081
Polymers59,0081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE PROTEASE NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0672
Polymers59,0081
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE PROTEASE NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0672
Polymers59,0081
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.550, 168.360, 98.800
Angle α, β, γ (deg.)90.00, 98.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.9995, -0.02716, -0.01318), (-0.02321, -0.4118, -0.911), (0.01931, 0.9109, -0.4122)-22.46, 19.35, 42.08
3given(0.8591, -0.1073, -0.5004), (-0.1037, -0.994, 0.0352), (-0.5012, 0.02164, -0.8651)24.22, -37.17, 97.39
4given(-0.8743, 0.09362, 0.4763), (0.04252, -0.9627, 0.2673), (0.4836, 0.2539, 0.8377)-49.01, -55.11, -34.82

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Components

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


Mass: 59007.828 Da / Num. of mol.: 4 / Fragment: HELICASE DOMAIN, 1782-2280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLASSICAL SWINE FEVER VIRUS / Strain: ALFORT / Description: VIRUS HOST, SUS SCROFA (PIG) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P19712, pestivirus NS3 polyprotein peptidase, nucleoside-triphosphate phosphatase, RNA helicase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Description: PEAK DATASET PEAK AND INFLECTION DATASET WERE COLLECTED WITH INVERSE BEAM DATA COLLECTION STRATEGY
Crystal growpH: 6.5
Details: 0.1 M NA-CACODYLATE 0.2 M MAGNESIUM ACETATE 12% PEG 8000, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9791
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.82→49.57 Å / Num. obs: 402065 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 47.94 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.2
Reflection shellResolution: 2.82→2.89 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 65

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Processing

Software
NameVersionClassification
BUSTER2.13.0refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.82→49.52 Å / Cor.coef. Fo:Fc: 0.8984 / Cor.coef. Fo:Fc free: 0.8628 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.311
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 2532 5.09 %RANDOM
Rwork0.1661 ---
obs0.1681 49698 90.65 %-
Displacement parametersBiso mean: 66.05 Å2
Baniso -1Baniso -2Baniso -3
1-13.8797 Å20 Å23.8296 Å2
2---32.1921 Å20 Å2
3---18.3124 Å2
Refine analyzeLuzzati coordinate error obs: 0.381 Å
Refinement stepCycle: LAST / Resolution: 2.82→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14731 0 8 122 14861
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115016HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1920306HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5336SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes390HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2137HARMONIC5
X-RAY DIFFRACTIONt_it15016HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1957SEMIHARMONIC5
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_contact17118SEMIHARMONIC4
LS refinement shellResolution: 2.82→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2638 104 4.91 %
Rwork0.2162 2013 -
all0.2185 2117 -
obs--90.65 %
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)
14.2817-0.6232-0.14292.6721.01226.50060.0261-0.7610.18060.2276-0.11880.4005-0.1823-0.74840.0926-0.1702-0.16860.06730.04340.0006-0.18367.389613.77879.0948
24.3943-0.08580.03712.8080.98354.91310.1034-0.266-0.07350.17730.112-0.18090.26510.091-0.2154-0.1451-0.0632-0.01320.07660.0301-0.247333.246238.543122.4765
33.6307-0.11861.39431.51050.23053.70590.0144-0.28240.08830.14420.0061-0.29970.22460.5909-0.0205-0.1389-0.10180.02450.030.0609-0.127138.57428.02264.4223
44.33730.45290.7884.1586-0.01425.02270.00490.56540.6071-0.62460.07280.1689-0.2789-0.4068-0.0777-0.1830.1518-0.037-0.00210.1015-0.133329.6533-30.2116.2537
58.6710.9256-0.33764.30950.44145.3538-0.1718-0.1140.9565-0.15050.0996-0.4647-0.80390.80370.0722-0.1863-0.13050.0318-0.1380.0164-0.144254.6369-25.4328-7.0463
64.69470.9287-0.62262.0047-0.69843.89960.0505-0.4040.54770.0348-0.0489-0.2825-0.2210.9218-0.0016-0.36220.0617-0.03660.1576-0.185-0.124960.5911-31.074324.6147
74.4063-0.1262-0.3181.52830.88523.4836-0.06121.12730.1371-0.38870.05230.26120.0641-0.70540.0089-0.1845-0.1563-0.10010.39030.192-0.25448.743641.669744.9648
84.79030.68230.9152.85580.76316.02580.07710.1883-0.12810.0660.0092-0.25540.27660.2077-0.0864-0.0312-0.1726-0.01770.06010.0082-0.203522.81616.587737.6311
93.3032-0.6737-1.58441.91531.06183.1734-0.02740.1708-0.1558-0.08570.103-0.17090.23530.1042-0.0756-0.1245-0.1149-0.0499-0.05760.0829-0.145336.300732.534658.3727
104.3596-0.3873-0.41274.63311.45463.46020.23470.53-0.5343-0.5688-0.1406-0.0960.49120.4546-0.09410.11320.0405-0.0618-0.19420.0237-0.198311.7427-7.355775.5066
115.63480.5056-1.3333.6046-0.25826.6545-0.67890.8644-0.43010.06580.26920.06440.993-1.45710.40970.0203-0.48610.07070.3726-0.1224-0.2762-5.1553-2.003846.2857
123.83750.28012.08061.2704-0.24935.5240.0627-0.04370.0549-0.17790.03580.29750.4662-0.9526-0.0985-0.1188-0.1617-0.058-0.08170.0442-0.0991-16.5498.279675.2981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|206 - A|352}
2X-RAY DIFFRACTION2{A|361 - A|474,A|491 - A|525}
3X-RAY DIFFRACTION3{A|475 - A|490, A|526-A|684}
4X-RAY DIFFRACTION4{B|205 - B|353}
5X-RAY DIFFRACTION5{B|361 - B|474}
6X-RAY DIFFRACTION6{ B|491 - B|525 }
7X-RAY DIFFRACTION7{B|475 - B|490,B|526 - B|684}
8X-RAY DIFFRACTION8{C|360 - C|474}
9X-RAY DIFFRACTION9{D|205 - D|353}
10X-RAY DIFFRACTION10{D|360 - D|474}
11X-RAY DIFFRACTION11{D|491 - D|525,D|360 - D|474}
12X-RAY DIFFRACTION12{D|475 - D|490,D|526 - D|683}

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