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- PDB-7z2j: White Bream virus N7-Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 7z2j
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
S-ADENOSYL-L-HOMOCYSTEINE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesWhite bream virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.657 Å
AuthorsShannon, A. / Gauffre, P. / Canard, B. / Ferron, F.
Funding support France, 2items
OrganizationGrant numberCountry
Other privateFondation pour la Recherche Medical
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 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7152
Polymers29,3301
Non-polymers3841
Water2,000111
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)41.586, 49.017, 53.763
Angle α, β, γ (deg.)90.000, 110.040, 90.000
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.76 Å3/Da / Density % sol: 29.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.1 M Tris pH 7.7, 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 1 / Wavelength: 1.25452 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25452 Å / Relative weight: 1
ReflectionResolution: 1.657→39.07 Å / Num. obs: 24275 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.66-1.750.5922194235080.9280.2540.6452.799.3
5.24-39.070.04150908070.9990.0170.04536.499.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDS20210323data reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Z05

7z05


Resolution: 1.657→39.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.099 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1174 4.84 %RANDOM
Rwork0.1862 ---
obs0.1875 24261 99.8 %-
Displacement parametersBiso max: 77.96 Å2 / Biso mean: 32.91 Å2 / Biso min: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1--5.9914 Å20 Å2-6.5956 Å2
2--8.382 Å20 Å2
3----2.3906 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.657→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 26 111 1877
Biso mean--35.58 42.09 -
Num. residues----225
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d601SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it1815HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion262SEMIHARMONIC5
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_contact1613SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1815HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2485HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion16.51
LS refinement shellResolution: 1.66→1.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3517 28 5.76 %
Rwork0.2721 458 -
all0.277 486 -
obs--96.48 %
Refinement TLS params.Method: refined / Origin x: 12.5247 Å / Origin y: 0.3974 Å / Origin z: 10.062 Å
111213212223313233
T-0.0706 Å20.0176 Å20.0488 Å2--0.134 Å20.0061 Å2---0.1008 Å2
L0.3909 °20.3982 °20.0175 °2-0.7316 °20.1083 °2--0.2679 °2
S0.0291 Å °-0.023 Å °-0.0042 Å °0.0198 Å °-0.0178 Å °0.0044 Å °-0.0509 Å °-0.0118 Å °-0.0113 Å °
Refinement TLS groupSelection details: { A|* }

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