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Basic information

Entry
Database: PDB / ID: 2xbm
TitleCrystal structure of the dengue virus methyltransferase bound to a 5'- capped octameric RNA
Components
  • 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
  • NONSTRUCTURAL PROTEIN NS5
KeywordsRNA BINDING PROTEIN / FLAVIVIRUS
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane / extracellular region / ATP binding / metal ion binding / nucleus
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 capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 / 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, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / Core protein
Similarity search - Component
Biological speciesDENGUE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.9 Å
AuthorsYap, L.J. / Luo, D.H. / Chung, K.Y. / Lim, S.P. / Bodenreider, C. / Noble, C. / Shi, P.Y. / Lescar, J.
CitationJournal: Plos One / Year: 2010
Title: Crystal Structure of the Dengue Virus Methyltransferase Bound to a 5'-Capped Octameric RNA
Authors: Yap, L.J. / Luo, D.H. / Chung, K.Y. / Lim, S.P. / Bodenreider, C. / Noble, C. / Shi, P.Y. / Lescar, J.
History
DepositionApr 13, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NONSTRUCTURAL PROTEIN NS5
B: NONSTRUCTURAL PROTEIN NS5
C: NONSTRUCTURAL PROTEIN NS5
D: NONSTRUCTURAL PROTEIN NS5
E: 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
F: 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,66824
Polymers125,7936
Non-polymers2,87518
Water8,323462
1
B: NONSTRUCTURAL PROTEIN NS5
D: NONSTRUCTURAL PROTEIN NS5
E: 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,33412
Polymers62,8973
Non-polymers1,4379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-105.1 kcal/mol
Surface area26100 Å2
MethodPISA
2
A: NONSTRUCTURAL PROTEIN NS5
C: NONSTRUCTURAL PROTEIN NS5
F: 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,33412
Polymers62,8973
Non-polymers1,4379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-96.7 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.543, 137.543, 109.385
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 263
2111B8 - 263
1121C8 - 263
2121D8 - 263

NCS ensembles :
ID
1
2

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Components

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Protein / RNA chain , 2 types, 6 molecules ABCDEF

#1: Protein
NONSTRUCTURAL PROTEIN NS5 / DENGUE VIRUS METHYLTRANSFERASE


Mass: 29796.275 Da / Num. of mol.: 4 / Fragment: METHYLTRANSFERASE, RESIDUES 2491-2753 / Source method: isolated from a natural source / Source: (natural) DENGUE VIRUS / References: UniProt: C0LMU5
#2: RNA chain 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3' / CAPPED RNA


Mass: 3303.991 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 480 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 4.59 Å3/Da / Density % sol: 73 % / Description: NONE
Crystal growpH: 5 / Details: PH 5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. obs: 50667 / % possible obs: 99 % / Observed criterion σ(I): 2.2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 2.2
Reflection shellHighest resolution: 2.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.9→39.71 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 27.681 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2572 5.1 %RANDOM
Rwork0.204 ---
obs0.205 48083 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8241 408 176 462 9287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2112.04712313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.67151037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63922.948363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.564151581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7181576
X-RAY DIFFRACTIONr_chiral_restr0.0990.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2171.55158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45128349
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7633897
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3864.53962
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2043tight positional0.010.05
12B2043tight positional0.010.05
21C2038tight positional0.020.05
22D2038tight positional0.020.05
11A2043tight thermal0.010.5
12B2043tight thermal0.010.5
21C2038tight thermal0.010.5
22D2038tight thermal0.010.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 206 -
Rwork0.328 3569 -
obs--99.47 %
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)
12.81450.0265-1.1272.38780.83734.30160.1605-0.1301-0.14560.2305-0.1241-0.04750.14060.2472-0.03640.2215-0.1361-0.04240.19860.04580.1745-16.641-12.1920.212
22.25170.42890.12452.4715-1.47094.2641-0.01120.3321-0.1061-0.05990.0444-0.10910.3014-0.0119-0.03320.101-0.060.01780.3399-0.05540.2029-49.852-31.387-23.767
33.34561.07560.46361.789-0.06064.470900.44320.1891-0.06480.03030.0536-0.1801-0.1915-0.03030.11170.0150.04380.40590.10060.2014-19.722-7.924-40.979
43.22131.13150.06892.05860.35244.51450.2195-0.17080.14760.3293-0.18120.1119-0.2508-0.0857-0.03840.3449-0.12490.11570.1645-0.00680.2099-52.015-26.60317.832
59.38720.55392.89540.23611.380114.4045-0.45461.38080.5952-0.14070.3208-0.0079-1.19990.63130.13390.67050.0528-0.22890.7666-0.28751.0867-26.235-41.906-16.704
62.25641.55813.26693.7358-3.074217.27120.8267-0.76080.01790.5581-0.0420.64530.3402-1.5083-0.78461.0635-0.0888-0.40190.95730.11781.3078-19.481-37.977-6.512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 263
2X-RAY DIFFRACTION2B6 - 263
3X-RAY DIFFRACTION3C5 - 263
4X-RAY DIFFRACTION4D5 - 263
5X-RAY DIFFRACTION5E0 - 8
6X-RAY DIFFRACTION6F0 - 8

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