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- PDB-7ziu: Crystal structure of Ntaya virus NS5 polymerase domain -

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Basic information

Entry
Database: PDB / ID: 7ziu
TitleCrystal structure of Ntaya virus NS5 polymerase domain
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / viral / polymerase / ns5
Function / homology
Function and homology information


ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity ...ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
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 non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / 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 capsid protein C / Flavivirus capsid protein C / 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 NS3 helicase, C-terminal helical 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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesNtaya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKrejcova, K. / Klima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2024
Title: Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase.
Authors: Krejcova, K. / Krafcikova, P. / Klima, M. / Chalupska, D. / Chalupsky, K. / Zilecka, E. / Boura, E.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 5, 2024Group: 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
Revision 1.3Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0866
Polymers146,8242
Non-polymers2624
Water00
1
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5433
Polymers73,4121
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5433
Polymers73,4121
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.285, 79.793, 133.255
Angle α, β, γ (deg.)90.000, 93.310, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Genome polyprotein


Mass: 73412.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ntaya virus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0BRZ6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 47.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG4000, 20% glycerol; 100 mM bicine/Trizma base pH 8.5; 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM D-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.8→47.58 Å / Num. obs: 33010 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 50.33 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.3472 / Rpim(I) all: 0.1419 / Rrim(I) all: 0.3757 / Net I/σ(I): 6.13
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.772 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3220 / CC1/2: 0.529 / CC star: 0.832 / Rpim(I) all: 0.7265 / Rrim(I) all: 1.918 / % possible all: 97.66

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Processing

Software
NameVersionClassification
XDSxdsgui2data reduction
XDSxdsgui2data scaling
PHASER2.8.3phasing
PHENIX1.20_4459refinement
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qsn

6qsn


Resolution: 2.8→47.58 Å / SU ML: 0.4307 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.5818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2887 1649 5 %random selection
Rwork0.2369 31348 --
obs0.2395 32997 98.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.33 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9728 0 4 0 9732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00179975
X-RAY DIFFRACTIONf_angle_d0.426413501
X-RAY DIFFRACTIONf_chiral_restr0.03761415
X-RAY DIFFRACTIONf_plane_restr0.00341724
X-RAY DIFFRACTIONf_dihedral_angle_d10.90113677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.46081290.37862457X-RAY DIFFRACTION94.45
2.88-2.970.40331360.33462590X-RAY DIFFRACTION98.66
2.97-3.080.32111370.33832610X-RAY DIFFRACTION98.35
3.08-3.20.40561380.30892620X-RAY DIFFRACTION98.96
3.2-3.350.33811360.28282589X-RAY DIFFRACTION99.09
3.35-3.520.32581390.26032642X-RAY DIFFRACTION99.29
3.52-3.750.25471370.23552600X-RAY DIFFRACTION98.99
3.75-4.030.2921360.21552608X-RAY DIFFRACTION98.6
4.03-4.440.25621400.20012650X-RAY DIFFRACTION99.47
4.44-5.080.24861380.18872636X-RAY DIFFRACTION99.5
5.08-6.40.26581400.22622652X-RAY DIFFRACTION98.83
6.4-47.580.22371430.18742694X-RAY DIFFRACTION98.68

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