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- PDB-2wv9: Crystal Structure of the NS3 protease-helicase from Murray Valley... -

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Basic information

Entry
Database: PDB / ID: 2wv9
TitleCrystal Structure of the NS3 protease-helicase from Murray Valley encephalitis virus
ComponentsFLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT, FLAVIVIRIN PROTEASE NS3 CATALYTIC SUBUNIT
KeywordsHYDROLASE / NUCLEOTIDE-BINDING / CAPSID PROTEIN / RNA REPLICATION / ENVELOPE PROTEIN / VIRION / HELICASE / FLAVIVIRUS / NUCLEOTIDYLTRANSFERASE
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Thrombin, subunit H - #120 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMURRAY VALLEY ENCEPHALITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAssenberg, R. / Mastrangelo, E. / Walter, T.S. / Verma, A. / Milani, M. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. / Mancini, E.J.
CitationJournal: J.Virol. / Year: 2009
Title: Crystal Structure of a Novel Conformational State of the Flavivirus Ns3 Protein: Implications for Polyprotein Processing and Viral Replication.
Authors: Assenberg, R. / Mastrangelo, E. / Walter, T.S. / Verma, A. / Milani, M. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. / Mancini, E.J.
History
DepositionOct 15, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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: FLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT, FLAVIVIRIN PROTEASE NS3 CATALYTIC SUBUNIT


Theoretical massNumber of molelcules
Total (without water)74,0571
Polymers74,0571
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.910, 105.460, 80.068
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT, FLAVIVIRIN PROTEASE NS3 CATALYTIC SUBUNIT


Mass: 74056.555 Da / Num. of mol.: 1 / Fragment: NS2B, RESIDUES 1421-1465
Source method: isolated from a genetically manipulated source
Details: PARTIAL POLYPROTEIN FRAGMENT OF NS2B FRAGMENT SEPARATED FROM NS3 BY A SEQUENCE ENCODING A NINE AMINO ACID LINKER (GGGGSGGGG).
Source: (gene. exp.) MURRAY VALLEY ENCEPHALITIS VIRUS / Strain: MVE-1-51 / Plasmid: OPPF4631 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3)PLYS / References: UniProt: P05769, flavivirin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 49-93 OF PROTEIN NS2B WERE LINKED TO RESIDUES 1-618 OF NS3 VIA A SYNTHETIC LINKER ...RESIDUES 49-93 OF PROTEIN NS2B WERE LINKED TO RESIDUES 1-618 OF NS3 VIA A SYNTHETIC LINKER (GGGGSGGGG) ADDED AT THE C-TERMINUS OF NS2B

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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: 2.29 Å3/Da / Density % sol: 46.39 % / Description: NONE
Crystal growDetails: 100 MM MES PH 6.0, 20% POLYETHYLENE GLYCOL 6000, 200 MM MAGNESIUM CHLORIDE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.1271
DetectorType: ADSC CCD / Detector: CCD / Date: May 14, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.75→43.937 Å / Num. obs: 17750 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.2
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2V8O, 2IJO

2v8o

2ijo


Resolution: 2.75→43.94 Å / Cor.coef. Fo:Fc: 0.858 / Cor.coef. Fo:Fc free: 0.844 / SU B: 37.435 / SU ML: 0.353 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.448 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3 884 5 %RANDOM
Rwork0.267 ---
obs0.268 16866 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å2-0.24 Å2
2--2.68 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.75→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 0 89 4766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.9466496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4315596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94523.349215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85415783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5161539
X-RAY DIFFRACTIONr_chiral_restr0.0590.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1690.21975
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23158
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1451.52977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.26724792
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.24631808
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4344.51704
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 66 -
Rwork0.324 1226 -
obs--98.1 %
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)
16.2672-1.88110.92121.99742.33199.5093-0.01370.0395-0.52250.27870.11160.16060.7028-0.1374-0.0980.29740.0630.0130.3084-0.04790.383627.45718.745-3.284
21.122-0.3592-0.32781.1232-0.78611.662-0.027-0.2287-0.2115-0.1027-0.05660.18190.3450.05280.08370.5660.0454-0.00940.5197-0.06030.4979-1.081.8436.051
338.01680.48492.25134.51756.468622.9086-2.05262.8624.9487-0.13390.4021-0.1866-2.9047-0.24621.65050.7643-0.0214-0.50650.32060.21310.930526.34728.893-8.085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 168
2X-RAY DIFFRACTION2A178 - 618
3X-RAY DIFFRACTION3A-52 - -33

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