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- PDB-7z05: White Bream virus N7-Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 7z05
TitleWhite Bream virus N7-Methyltransferase
ComponentsNon-structural protein 1
KeywordsTRANSFERASE / N7-methyl transferase / capping enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / cysteine-type peptidase activity / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / DNA helicase ...Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / cysteine-type peptidase activity / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / DNA helicase / RNA helicase activity / Hydrolases; Acting on ester bonds / membrane => GO:0016020 / RNA helicase / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
SF1 helicase, zinc-binding domain, tornidovirus / Methyltransferase domain 25 / Methyltransferase domain / Viral (Superfamily 1) RNA helicase / Nidovirus 2-O-methyltransferase / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase ...SF1 helicase, zinc-binding domain, tornidovirus / Methyltransferase domain 25 / Methyltransferase domain / Viral (Superfamily 1) RNA helicase / Nidovirus 2-O-methyltransferase / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Serine proteases, trypsin family, serine active site. / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesWhite bream virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å
AuthorsShannon, A. / Gauffre, P. / Canard, B. / Ferron, F.
Funding support France, 2items
OrganizationGrant numberCountry
Other privateFondation pour la Recherche Medical France
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-01 France
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome.
Authors: Shannon, A. / Sama, B. / Gauffre, P. / Guez, T. / Debart, F. / Vasseur, J.J. / Decroly, E. / Canard, B. / Ferron, F.
History
DepositionFeb 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9505
Polymers29,3301
Non-polymers6204
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.216, 49.787, 53.926
Angle α, β, γ (deg.)90.000, 97.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-structural protein 1 / nsp1


Mass: 29330.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) White bream virus / Strain: isolate Blicca bjoerkna L./Germany/DF24/00 / Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q008X6
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1 M Tris, 20.3 % PEG 3350, 0.2 M MgCl and 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.992 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.33→52.13 Å / Num. obs: 12026 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.142 / Net I/σ(I): 9.9 / Num. measured all: 80985 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.33-2.456.80.9241174217390.8930.3831.0022.499.9
7.36-52.136.30.04125524060.9990.0170.04427.399.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS20200131data reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alpha fold 2

Resolution: 2.33→52.13 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 586 4.88 %
Rwork0.2114 11412 -
obs0.214 11998 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.78 Å2 / Biso mean: 55.2715 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.33→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 41 74 1994
Biso mean--54.86 51.57 -
Num. residues----239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.560.34861450.294528132958100
2.56-2.930.32381470.242328372984100
2.93-3.690.25521530.211528422995100
3.69-52.130.23621410.18592920306199

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