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- PDB-6kr3: Crystal structure of Dengue virus nonstructural protein NS5 (form 2) -

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Basic information

Entry
Database: PDB / ID: 6kr3
TitleCrystal structure of Dengue virus nonstructural protein NS5 (form 2)
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / polymerase / methyltransferase
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / 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, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.931 Å
AuthorsWu, J. / Lu, G. / Ye, H.Q. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2018YFA0507200 China
CitationJournal: Plos Pathog. / Year: 2020
Title: A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase.
Authors: Wu, J. / Ye, H.Q. / Zhang, Q.Y. / Lu, G. / Zhang, B. / Gong, P.
History
DepositionAug 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

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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)213,24930
Polymers209,0862
Non-polymers4,16328
Water84747
1
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,15019
Polymers104,5431
Non-polymers2,60718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,10011
Polymers104,5431
Non-polymers1,55710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.845, 209.975, 157.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Genome polyprotein


Mass: 104543.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q91H74

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Non-polymers , 5 types, 75 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.54 Å3/Da / Density % sol: 65.3 % / Mosaicity: 0.343 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.1 / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.93→60 Å / Num. obs: 63847 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 64.31 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.064 / Rrim(I) all: 0.153 / Χ2: 1.033 / Net I/σ(I): 6.1 / Num. measured all: 356093
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.93-3.035.50.5563040.8320.2570.6090.988100
3.03-3.165.30.39163210.8960.1890.4361.053100
3.16-3.35.80.30563240.9390.1390.3361.059100
3.3-3.475.80.22963250.9630.1040.2521.026100
3.47-3.695.80.18163580.9720.0820.1991.01299.9
3.69-3.985.50.14963350.9780.070.1651.00399.9
3.98-4.385.50.12863930.9820.060.1421.0499.9
4.38-5.015.80.11863800.9850.0540.131.01799.9
5.01-6.315.40.11364680.9830.0540.1251.045100
6.31-605.40.09266390.990.0440.1021.08299.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6M, 4V0Q

4k6m

4v0q


Resolution: 2.931→49.812 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.38
RfactorNum. reflection% reflection
Rfree0.2681 3164 4.96 %
Rwork0.2333 --
obs0.235 63805 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.69 Å2 / Biso mean: 60.351 Å2 / Biso min: 22.63 Å2
Refinement stepCycle: final / Resolution: 2.931→49.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12757 0 153 47 12957
Biso mean--63.56 52.59 -
Num. residues----1678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01213191
X-RAY DIFFRACTIONf_angle_d1.23417940
X-RAY DIFFRACTIONf_chiral_restr0.0651956
X-RAY DIFFRACTIONf_plane_restr0.0072311
X-RAY DIFFRACTIONf_dihedral_angle_d22.1977731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.931-2.97460.38581240.3465256999
2.9746-3.02110.39891180.33092631100
3.0211-3.07060.34991240.29582620100
3.0706-3.12360.29631430.27992611100
3.1236-3.18030.31921500.28622612100
3.1803-3.24150.34631550.28792601100
3.2415-3.30770.34521230.28842615100
3.3077-3.37960.31151420.27642631100
3.3796-3.45820.35211530.27222592100
3.4582-3.54460.31481370.25422616100
3.5446-3.64040.2651220.24782633100
3.6404-3.74750.30831260.23562660100
3.7475-3.86840.2621520.23412588100
3.8684-4.00660.2941470.22532597100
4.0066-4.1670.26911360.22182656100
4.167-4.35650.22711480.20162616100
4.3565-4.58610.24191420.1942636100
4.5861-4.87320.21351370.19442651100
4.8732-5.2490.25251390.21032659100
5.249-5.77660.26041340.23652667100
5.7766-6.61080.20991350.22022682100
6.6108-8.32260.26081420.21322685100
8.3226-49.8120.20851350.21162813100

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