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- PDB-2v8o: Structure of the Murray Valley encephalitis virus RNA helicase to... -

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Basic information

Entry
Database: PDB / ID: 2v8o
TitleStructure of the Murray Valley encephalitis virus RNA helicase to 1. 9A resolution
ComponentsFLAVIVIRIN PROTEASE NS3
KeywordsHYDROLASE / MURRAY VALLEY ENCEPHALITIS VIRUS / GLYCOPROTEIN / VIRAL ENZYMES / TRANSMEMBRANE / CLEAVAGE ON PAIR OF BASIC RESIDUES / ATP-BINDING / TRANSFERASE / FLAVIVIRIDAE / CORE PROTEIN / VIRION / MEMBRANE / HELICASE / HELICASES / CAPSID PROTEIN / RNA REPLICATION / ENVELOPE PROTEIN / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE / RNA-DIRECTED RNA POLYMERASE
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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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
: / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / : / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMURRAY VALLEY ENCEPHALITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMancini, E.J. / Assenberg, R. / Verma, A. / Walter, T.S. / Tuma, R. / Grimes, J.M. / Owens, R.J. / Stuart, D.I.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of the Murray Valley Encephalitis Virus RNA Helicase at 1.9 A Resolution.
Authors: Mancini, E.J. / Assenberg, R. / Verma, A. / Walter, T.S. / Tuma, R. / Grimes, J.M. / Owens, R.J. / Stuart, D.I.
History
DepositionAug 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 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

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Assembly

Deposited unit
A: FLAVIVIRIN PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)49,8591
Polymers49,8591
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.516, 76.414, 70.609
Angle α, β, γ (deg.)90.00, 91.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FLAVIVIRIN PROTEASE NS3 / NS3 HELICASE


Mass: 49858.594 Da / Num. of mol.: 1 / Fragment: NS3 HELICASE DOMAIN, RESIDUES 1681-2122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MURRAY VALLEY ENCEPHALITIS VIRUS / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P05769, flavivirin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN UNDER STUDY IS THE NS3 HELICASE DOMAIN OF THE BIFUNCTIONAL NS3 PROTEASE-HELICASE (NP_ ...THE PROTEIN UNDER STUDY IS THE NS3 HELICASE DOMAIN OF THE BIFUNCTIONAL NS3 PROTEASE-HELICASE (NP_722535) PROTEIN OF MURRAY VALLEY ENCEPHALITIS VIRUS N-TERMINAL RESIDUES GLY, PRO ARE CLONING PRODUCTS.

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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: 2.21 Å3/Da / Density % sol: 44.49 % / Description: NONE
Crystal growpH: 7 / Details: 5% PEG6000, 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC CCD / Detector: CCD / Date: May 16, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 36088 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMF

2bmf


Resolution: 1.9→70.53 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.389 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1789 5 %RANDOM
Rwork0.18 ---
obs0.182 33827 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.9→70.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 0 284 3667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223460
X-RAY DIFFRACTIONr_bond_other_d0.0010.022398
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9534693
X-RAY DIFFRACTIONr_angle_other_deg0.8735806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35623.168161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96815582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1081532
X-RAY DIFFRACTIONr_chiral_restr0.0710.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_nbd_refined0.2140.2726
X-RAY DIFFRACTIONr_nbd_other0.1980.22575
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21678
X-RAY DIFFRACTIONr_nbtor_other0.0830.21774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2170.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.71142773
X-RAY DIFFRACTIONr_mcbond_other1.1664861
X-RAY DIFFRACTIONr_mcangle_it4.04853450
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.10451554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.45861243
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 164 -
Rwork0.205 2456 -
obs--100 %
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)
10.5793-0.54640.04052.46450.02550.8879-0.0251-0.1085-0.02980.33740.01530.12460.088-0.0310.0098-0.0405-0.04430.003-0.03110.0056-0.066132.415-1.29616.215
20.8727-0.5-3.42853.10750.635914.09430.1864-0.696-0.31080.4930.20230.4217-0.4317-0.9622-0.38870.18750.03760.17070.1393-0.0123-0.021723.9724.02341.04
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 550
2X-RAY DIFFRACTION2A551 - 618

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