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- PDB-2oxt: Crystal structure of Meaban virus nucleoside-2'-O-methyltransferase -

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Basic information

Entry
Database: PDB / ID: 2oxt
TitleCrystal structure of Meaban virus nucleoside-2'-O-methyltransferase
ComponentsNUCLEOSIDE-2'-O-METHYLTRANSFERASE
KeywordsVIRAL PROTEIN / Flavivirus / nucleoside-2'-O-methyltransferase / Viral enzyme / RNA capping / S-adenosyl-L-Methionine
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
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. ...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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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 / Vaccinia Virus protein VP39 / 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-ADENOSYLMETHIONINE / Genome polyprotein
Similarity search - Component
Biological speciesMeaban virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMastrangelo, E. / Milani, M. / Bollati, M. / Bolognesi, M.
CitationJournal: Protein Sci. / Year: 2007
Title: Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase
Authors: Mastrangelo, E. / Bollati, M. / Milani, M. / Selisko, B. / Peyrane, F. / Canard, B. / Grard, G. / de Lamballerie, X. / Bolognesi, M.
History
DepositionFeb 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
B: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
C: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
D: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,1868
Polymers118,5924
Non-polymers1,5944
Water905
1
A: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0472
Polymers29,6481
Non-polymers3981
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0472
Polymers29,6481
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0472
Polymers29,6481
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NUCLEOSIDE-2'-O-METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0472
Polymers29,6481
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.977, 82.977, 170.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
NUCLEOSIDE-2'-O-METHYLTRANSFERASE


Mass: 29648.100 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: complex with S-adenosyl-L-Methionine / Source: (gene. exp.) Meaban virus / Genus: Flavivirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0EKU1
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEGMME 2000, nickel chloride 0.01M, Tris 0.1 M , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2006
Details: Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror
RadiationMonochromator: high resolution Si(311) cut and a lower resolution Si(111) cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. all: 24302 / Num. obs: 24302 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3582 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R6A

1r6a


Resolution: 2.9→37.85 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.841 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30597 1213 5 %RANDOM
Rwork0.23071 ---
all0.23444 24302 --
obs0.23444 23074 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.639 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2---3.66 Å20 Å2
3---7.32 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8296 0 108 5 8409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228576
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.97511568
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25351056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29121.573356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.5151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.94215100
X-RAY DIFFRACTIONr_chiral_restr0.070.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.24005
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25652
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.45925236
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84838412
X-RAY DIFFRACTIONr_scbond_it1.09623340
X-RAY DIFFRACTIONr_scangle_it1.96833156
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 86 -
Rwork0.301 1710 -
obs--96.72 %

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