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- PDB-6yu8: RNA Methyltransferase of Sudan Ebola Virus -

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Basic information

Entry
Database: PDB / ID: 6yu8
TitleRNA Methyltransferase of Sudan Ebola Virus
Components
  • Methyltransferase domain of the L protein
  • VHH antiboby
KeywordsTRANSFERASE / RNA Methyltransferase / Virus / Ebola / L protein
Function / homology
Function and homology information


negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity ...negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding
Similarity search - Function
RNA-directed RNA polymerase L, filovirus / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesSudan virus - Boniface
Sudan
1976
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.841 Å
AuthorsFerron, F. / Valle, C. / Zamboni, V. / Canard, B. / Decroly, E.
Funding support France, 3items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
French National Research AgencyANR-16_CE11_0031_01 France
French Ministry of Armed Forces2009.34.0038 France
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: First insights into the structural features of Ebola virus methyltransferase activities.
Authors: Valle, C. / Martin, B. / Ferron, F. / Roig-Zamboni, V. / Desmyter, A. / Debart, F. / Vasseur, J.J. / Canard, B. / Coutard, B. / Decroly, E.
History
DepositionApr 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 4, 2021Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase domain of the L protein
B: VHH antiboby
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,99427
Polymers49,7152
Non-polymers1,27925
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-159 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.761, 153.761, 105.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-2384-

HOH

21A-2485-

HOH

31A-2496-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Methyltransferase domain of the L protein


Mass: 35632.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan virus - Boniface, Sudan,1976 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XX01*PLUS
#2: Antibody VHH antiboby


Mass: 14082.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lama glama (llama)

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Non-polymers , 6 types, 454 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% PEG 20000 Tris 0.1M NaCl 0,15M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28242 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28242 Å / Relative weight: 1
ReflectionResolution: 1.841→82.622 Å / Num. obs: 63696 / % possible obs: 100 % / Redundancy: 40 % / CC1/2: 0.996 / Net I/σ(I): 13.7
Reflection shellResolution: 1.841→1.873 Å / Redundancy: 41 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3136 / CC1/2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (29-NOV-2019)refinement
PDB_EXTRACT3.25data extraction
XDS20190315data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gkd

6gkd


Resolution: 1.841→82.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.098 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 3165 4.97 %RANDOM
Rwork0.1949 ---
obs0.1959 63695 100 %-
Displacement parametersBiso max: 148.59 Å2 / Biso mean: 39.24 Å2 / Biso min: 21.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.7624 Å20 Å20 Å2
2---0.7624 Å20 Å2
3---1.5249 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.841→82.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3051 0 83 429 3563
Biso mean--63.54 54.02 -
Num. residues----390
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1095SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes525HARMONIC5
X-RAY DIFFRACTIONt_it3185HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2998SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3195HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4326HARMONIC20.91
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion14.27
LS refinement shellResolution: 1.841→1.85 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2452 69 5.42 %
Rwork0.2146 1205 -
obs--99.24 %
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)
10.28830.0718-0.16130.24940.03810.24250.02720.0603-0.0512-0.0319-0.0563-0.0182-0.04380.04810.0291-0.02020.00550.0079-0.0428-0.0134-0.049106.999441.689612.3691
21.27340.3067-0.43512.68910.89052.37310.0065-0.0291-0.08060.0554-0.09940.22930.5-0.1180.09280.0716-0.03340.0172-0.1411-0.0683-0.059992.76828.243513.9206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1755 - 2042
2X-RAY DIFFRACTION2{ B|* }B1 - 122

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