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- PDB-2px4: Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-... -

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Basic information

Entry
Database: PDB / ID: 2px4
TitleCrystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 2)
ComponentsGenome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]
KeywordsTRANSFERASE / Murray Valley Encephalitis Virus / Methyltransferase / SAH / Structural Genomics / Oxford Protein Production Facility / OPPF
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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / 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, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / Vaccinia Virus protein VP39 / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesMurray valley encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAssenberg, R. / Ren, J. / Verma, A. / Walter, T.S. / Alderton, D. / Hurrelbrink, R.J. / Fuller, S.D. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. / Oxford Protein Production Facility (OPPF)
CitationJournal: J.Gen.Virol. / Year: 2007
Title: Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues.
Authors: Assenberg, R. / Ren, J. / Verma, A. / Walter, T.S. / Alderton, D. / Hurrelbrink, R.J. / Fuller, S.D. / Bressanelli, S. / Owens, R.J. / Stuart, D.I. / Grimes, J.M.
History
DepositionMay 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600 HETEROGEN AUTHORS STATE THAT THE UNKNOWN ATOMS UNX801-UNX809 MARK THE POSITION IN ELECTRON DENSITY ... HETEROGEN AUTHORS STATE THAT THE UNKNOWN ATOMS UNX801-UNX809 MARK THE POSITION IN ELECTRON DENSITY AND BELONG TO AN UNKNOWN CHEMICAL GROUP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56222
Polymers30,3071
Non-polymers1,25521
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.400, 68.200, 50.200
Angle α, β, γ (deg.)90.00, 115.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)]


Mass: 30306.852 Da / Num. of mol.: 1
Fragment: NS5 2'-O Methyltransferase Domain: Residues 2530-2798
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murray valley encephalitis virus (strain MVE-1-51)
Genus: Flavivirus / Species: Murray Valley encephalitis virus / Strain: MVE-1-51, MVEV / Gene: NS5 / Plasmid: OPPF2936 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P05769, RNA-directed RNA polymerase

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Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 9 / Source method: obtained synthetically
#5: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Magnesium sulfate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 30, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 13890 / % possible obs: 96.5 % / Observed criterion σ(I): -1.5 / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1109 / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PX2

2px2


Resolution: 2.2→26.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.128 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS program has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.22927 676 4.9 %RANDOM
Rwork0.16138 ---
obs0.16463 13226 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.592 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å21.95 Å2
2---0.9 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2074 0 79 180 2333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222177
X-RAY DIFFRACTIONr_bond_other_d0.0020.021555
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9922930
X-RAY DIFFRACTIONr_angle_other_deg0.7833754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7722.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27315395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.011522
X-RAY DIFFRACTIONr_chiral_restr0.0590.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.1830.2424
X-RAY DIFFRACTIONr_nbd_other0.1820.21634
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21025
X-RAY DIFFRACTIONr_nbtor_other0.0810.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.217
X-RAY DIFFRACTIONr_mcbond_it3.50141690
X-RAY DIFFRACTIONr_mcbond_other0.8964539
X-RAY DIFFRACTIONr_mcangle_it3.70162072
X-RAY DIFFRACTIONr_scbond_it5.50561056
X-RAY DIFFRACTIONr_scangle_it7.27610858
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 40 -
Rwork0.16 753 -
obs--75.17 %
Refinement TLS params.Method: refined / Origin x: 9.835 Å / Origin y: -0.077 Å / Origin z: 20.913 Å
111213212223313233
T-0.1393 Å2-0.0251 Å2-0.0192 Å2--0.1697 Å2-0.0085 Å2---0.1641 Å2
L3.0855 °2-0.7782 °2-0.7458 °2-1.4315 °20.149 °2--0.7063 °2
S0.0316 Å °-0.0492 Å °0.0673 Å °0.0107 Å °-0.0171 Å °-0.0761 Å °-0.0044 Å °-0.0119 Å °-0.0146 Å °

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