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- PDB-7d6n: Crystal structure of tick-borne encephalitis virus RNA-dependent ... -

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Basic information

Entry
Database: PDB / ID: 7d6n
TitleCrystal structure of tick-borne encephalitis virus RNA-dependent RNA polymerase
ComponentsTick-borne encephalitis virus RNA-dependent RNA polymerase
KeywordsTRANSFERASE / polymerase
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. ...Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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
Biological speciesTick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.168 Å
AuthorsYang, J. / Jing, X. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure of tick-borne encephalitis virus
Authors: Yang, J. / Jing, X. / Zhang, B. / Zheng, Z. / Gong, P.
History
DepositionOct 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Tick-borne encephalitis virus RNA-dependent RNA polymerase
B: Tick-borne encephalitis virus RNA-dependent RNA polymerase
E: Tick-borne encephalitis virus RNA-dependent RNA polymerase
D: Tick-borne encephalitis virus RNA-dependent RNA polymerase
C: Tick-borne encephalitis virus RNA-dependent RNA polymerase
F: Tick-borne encephalitis virus RNA-dependent RNA polymerase
G: Tick-borne encephalitis virus RNA-dependent RNA polymerase
J: Tick-borne encephalitis virus RNA-dependent RNA polymerase
I: Tick-borne encephalitis virus RNA-dependent RNA polymerase
H: Tick-borne encephalitis virus RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)737,16840
Polymers735,61710
Non-polymers1,55130
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27080 Å2
ΔGint-504 kcal/mol
Surface area225790 Å2
Unit cell
Length a, b, c (Å)175.988, 235.181, 327.433
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tick-borne encephalitis virus RNA-dependent RNA polymerase / Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 ...Envelope protein E / Flavivirin protease NS2B regulatory subunit / Flavivirin protease NS3 catalytic subunit / Genome polyprotein / Matrix protein / Non-structural protein 1 / Non-structural protein 2A / Non-structural protein 2B / Non-structural protein 3 / Non-structural protein 4A / Non-structural protein 4B / Peptide 2k / Peptide pr / Protein prM / RNA-directed RNA polymerase NS5 / Serine protease NS3 / Serine protease subunit NS2B / Small envelope protein M


Mass: 73561.695 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus / Strain: WH2012 / Gene: NS5 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): CondonPlus-RIL / References: UniProt: K4P8A2, RNA-directed DNA polymerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: 4.61 Å3/Da / Density % sol: 73.29 %
Crystal growTemperature: 278 K / Method: evaporation / pH: 7.5 / Details: 5/4 PO/OH, magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.16→50 Å / Num. obs: 225446 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 77.98 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.054 / Rrim(I) all: 0.098 / Χ2: 0.939 / Net I/σ(I): 9.3 / Num. measured all: 721646
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.16-3.273.30.642226070.6280.4190.770.89199.5
3.27-3.43.20.431225760.7870.2840.5180.90499.1
3.4-3.563.10.282222900.8930.1860.340.9398.1
3.56-3.753.10.182221610.9530.1190.2190.93297.2
3.75-3.983.30.123227500.9790.0790.1470.97799.8
3.98-4.293.30.083227120.990.0540.0990.92599.5
4.29-4.723.20.055226780.9950.0360.0660.89399
4.72-5.430.047222530.9960.0310.0570.94796.9
5.4-6.83.30.042229180.9970.0270.050.96698.9
6.8-503.10.026225010.9990.0170.0311.02894.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829_000refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6M

4k6m


Resolution: 3.168→49.987 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 11328 5.03 %
Rwork0.1953 214001 -
obs0.1972 225329 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217.03 Å2 / Biso mean: 65.8132 Å2 / Biso min: 23.33 Å2
Refinement stepCycle: final / Resolution: 3.168→49.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45309 0 30 0 45339
Biso mean--67.78 --
Num. residues----5858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01146408
X-RAY DIFFRACTIONf_angle_d1.32663055
X-RAY DIFFRACTIONf_chiral_restr0.0926828
X-RAY DIFFRACTIONf_plane_restr0.0088100
X-RAY DIFFRACTIONf_dihedral_angle_d10.55728145
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1682-3.20420.32973410.2954668392
3.2042-3.24190.3323860.2777712799
3.2419-3.28140.31953770.26477193100
3.2814-3.32290.29424100.2505714399
3.3229-3.36670.34150.2402708499
3.3667-3.41280.26533990.2305714499
3.4128-3.46150.27243710.2323711799
3.4615-3.51320.29713840.2334707298
3.5132-3.5680.2633540.2278707598
3.568-3.62650.27183800.2074687096
3.6265-3.6890.25093680.2113695696
3.689-3.75610.2723710.21077235100
3.7561-3.82830.24993510.2017235100
3.8283-3.90640.24953750.19237246100
3.9064-3.99130.21673460.18417266100
3.9913-4.08410.23533600.19047257100
4.0841-4.18620.23083910.1791720199
4.1862-4.29940.20763720.1703716099
4.2994-4.42580.20333920.1685721299
4.4258-4.56860.20083740.1642716899
4.5686-4.73170.21013970.167721299
4.7317-4.9210.213750.1789718299
4.921-5.14480.22393680.1894716898
5.1448-5.41570.22613750.1943683794
5.4157-5.75450.23363810.1989722398
5.7545-6.19810.22574110.2062726299
6.1981-6.82050.23353730.1954730299
6.8205-7.80420.19924200.177719998
7.8042-9.82020.18433670.1537715896
9.8202-49.9870.22863440.2066701491

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