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- PDB-4cbh: Pestivirus NS3 helicase -

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Basic information

Entry
Database: PDB / ID: 4cbh
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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / monoatomic ion transmembrane transport / host cell surface / entry receptor-mediated virion attachment to host cell / host cell cytoplasm ...pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / monoatomic ion transmembrane transport / host cell surface / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / viral protein processing / RNA helicase / symbiont entry into host cell / 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 / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCLASSICAL SWINE FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 1.3Oct 14, 2015Group: Refinement description
Revision 1.4Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
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
Water13,836768
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)70.070, 144.440, 118.690
Angle α, β, γ (deg.)90.00, 92.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.8159, -0.5781, -0.008363), (-0.578, -0.8154, -0.03218), (0.01179, 0.03109, -0.9994)16, 49.25, 54.59
3given(-0.9998, -0.004143, 0.01775), (0.005176, -0.9983, 0.05858), (0.01747, 0.05866, 0.9981)29.15, 42.24, -1.335
4given(-0.7941, 0.6078, -0.003618), (0.6076, 0.7937, -0.02796), (-0.01412, -0.0244, -0.9996)13.34, -3.866, 56.72

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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, 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


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.68 Å3/Da / Density % sol: 54.04 % / Description: NONE
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: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→44.34 Å / Num. obs: 71319 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 63.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.51→2.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / % possible all: 49.6

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Processing

Software
NameVersionClassification
BUSTER2.13.0refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CBG

4cbg


Resolution: 2.51→72.22 Å / Cor.coef. Fo:Fc: 0.9197 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3572 5.01 %RANDOM
Rwork0.2034 ---
obs0.2048 71319 88.63 %-
Displacement parametersBiso mean: 60.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.7644 Å20 Å2-0.367 Å2
2--2.287 Å20 Å2
3----1.5227 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.51→72.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11023 0 0 768 11791
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111239HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2815196HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4015SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1598HARMONIC5
X-RAY DIFFRACTIONt_it11239HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion21.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1482SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13421SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2759 118 5.26 %
Rwork0.2432 2125 -
all0.245 2243 -
obs--88.63 %
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)
12.6191-0.1274-0.2721.8936-0.58373.1520.0655-0.518-0.19210.26730.12030.1752-0.2652-0.2927-0.1858-0.163-0.04060.0123-0.03730.0662-0.0511-2.8678-0.69146.6993
22.0786-0.25140.40871.8334-0.70162.80720.0338-0.3689-0.04190.2141-0.0137-0.2564-0.00420.5364-0.0201-0.2698-0.0367-0.0489-0.0376-0.0107-0.096828.0079-4.034540.7464
33.98420.0862-0.82251.4096-0.35114.58390.28490.93010.3302-0.3603-0.14430.1989-0.3984-0.9336-0.1406-0.16510.157-0.0203-0.00280.0799-0.173513.390551.64549.8015
42.87780.1254-0.44461.6179-0.04581.49930.02930.2757-0.2022-0.0919-0.0338-0.21240.04760.06690.0045-0.1230.0133-0.0093-0.1842-0.0192-0.068240.346235.663515.7121
51.5946-0.30670.17031.63920.99493.42430.0737-0.41430.21990.29550.0358-0.12020.30060.2866-0.1095-0.1351-0.0769-0.0202-0.0674-0.0618-0.092231.814444.776247.0159
62.2958-0.5681-0.58282.04240.69492.28920.0328-0.33610.12260.1798-0.11840.2058-0.0066-0.6310.0856-0.2775-0.04910.02430.0114-0.0759-0.1240.956148.271241.0165
71.6505-0.3824-1.63191.30530.24324.08940.05410.2904-0.2008-0.3075-0.0159-0.050.14960.2279-0.0382-0.1020.0133-0.0073-0.1475-0.0822-0.038616.2987-6.70879.2617
86.921.8603-8.82330.8734-6.95392.32130.03020.1734-0.0586-0.25070.33810.12220.17550.1972-0.3684-0.0727-0.30320.01470.7218-0.1353-0.34035.311117.6218-9.0749
91.4614-0.68020.21181.5314-0.23211.83040.15310.1484-0.0248-0.12420.02640.2550.0907-0.2699-0.1795-0.2380.0022-0.023-0.20320.0387-0.0972-11.93187.90616.4174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|202 - A|351}
2X-RAY DIFFRACTION2{A|471 - A|496,A|526 - A|682}
3X-RAY DIFFRACTION3{B|206 - B|351}
4X-RAY DIFFRACTION4{B|471 - B|496,B|526 - B|687}
5X-RAY DIFFRACTION5{C|205 - C|351}
6X-RAY DIFFRACTION6{C|471 - C|496,C|526 - C|681}
7X-RAY DIFFRACTION7{D|202 - D|351}
8X-RAY DIFFRACTION8{D|366 - D|474,D|491 - D|525}
9X-RAY DIFFRACTION9{D|475 - D|490,D|526 - D|688}

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