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- PDB-7xd9: Crystal Structure of Dengue Virus serotype 2 (DENV2) Polymerase E... -

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Basic information

Entry
Database: PDB / ID: 7xd9
TitleCrystal Structure of Dengue Virus serotype 2 (DENV2) Polymerase Elongation Complex (CTP Form)
Components
  • NS5
  • RNA (30-mer)
  • RNA (9-mer)
KeywordsTRANSFERASE/RNA / RNA-dependent RNA polymerase / de novo synthesis / elongation complex / priming element / TRANSFERASE / TRANSFERASE-RNA complex
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
CYTIDINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsWu, J. / Wang, X. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
National Natural Science Foundation of China (NSFC)32070185 China
National Natural Science Foundation of China (NSFC)32000136 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases.
Authors: Wu, J. / Wang, X. / Liu, Q. / Lu, G. / Gong, P.
History
DepositionMar 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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: NS5
B: RNA (30-mer)
C: RNA (9-mer)
D: NS5
E: RNA (30-mer)
F: RNA (9-mer)
G: NS5
H: RNA (30-mer)
I: RNA (9-mer)
J: NS5
K: RNA (30-mer)
L: RNA (9-mer)
M: NS5
N: RNA (30-mer)
O: RNA (9-mer)
P: NS5
Q: RNA (30-mer)
R: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)530,75860
Polymers525,67718
Non-polymers5,08142
Water8,899494
1
A: NS5
B: RNA (30-mer)
C: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,46010
Polymers87,6133
Non-polymers8477
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-66 kcal/mol
Surface area25700 Å2
MethodPISA
2
D: NS5
E: RNA (30-mer)
F: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,82814
Polymers87,6133
Non-polymers1,21511
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-73 kcal/mol
Surface area25870 Å2
MethodPISA
3
G: NS5
H: RNA (30-mer)
I: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3689
Polymers87,6133
Non-polymers7556
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-68 kcal/mol
Surface area25250 Å2
MethodPISA
4
J: NS5
K: RNA (30-mer)
L: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,46010
Polymers87,6133
Non-polymers8477
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-72 kcal/mol
Surface area26030 Å2
MethodPISA
5
M: NS5
N: RNA (30-mer)
O: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3689
Polymers87,6133
Non-polymers7556
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-69 kcal/mol
Surface area26440 Å2
MethodPISA
6
P: NS5
Q: RNA (30-mer)
R: RNA (9-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2758
Polymers87,6133
Non-polymers6635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-64 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.430, 154.580, 172.351
Angle α, β, γ (deg.)90.000, 94.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ADGJMP

#1: Protein
NS5


Mass: 75110.281 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q91H74

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RNA chain , 2 types, 12 molecules BEHKNQCFILOR

#2: RNA chain
RNA (30-mer)


Mass: 9621.792 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain
RNA (9-mer)


Mass: 2880.774 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 536 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 3.52 Å3/Da / Density % sol: 65.07 % / Mosaicity: 0.377 °
Crystal growTemperature: 289 K / Method: evaporation / Details: Sodium formate, Glycerol

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. obs: 230467 / % possible obs: 99.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 58.47 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.052 / Χ2: 0.951 / Net I/σ(I): 16 / Num. measured all: 750342
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.673.20.495229080.8060.3260.5940.91499.8
2.67-2.783.40.367229990.880.2350.4370.908100
2.78-2.913.40.238230400.950.1540.2840.913100
2.91-3.063.30.154229900.9750.10.1840.92100
3.06-3.253.10.09229420.9890.060.1090.96399.5
3.25-3.53.30.059230650.9950.0380.070.93499.9
3.5-3.853.20.039230600.9970.0260.0470.93599.8
3.85-4.413.30.031231050.9980.020.0370.94199.9
4.41-5.563.20.027231120.9980.0180.0330.94299.7
5.56-503.10.023232460.9990.0150.0271.15699.1

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6M

4k6m


Resolution: 2.58→48.84 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 11436 5.02 %
Rwork0.1911 216252 -
obs0.1926 227688 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.65 Å2 / Biso mean: 64.4885 Å2 / Biso min: 32.5 Å2
Refinement stepCycle: final / Resolution: 2.58→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29182 2889 270 494 32835
Biso mean--67.25 57.38 -
Num. residues----3867
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.58-2.610.38914140.318471427556100
2.61-2.640.30933450.295472457590100
2.64-2.670.35273370.274672327569100
2.67-2.710.30233820.264271587540100
2.71-2.740.32353990.259272347633100
2.74-2.780.28833840.254772137597100
2.78-2.820.28843850.246671737558100
2.82-2.860.28733940.245172167610100
2.86-2.910.28383870.243672027589100
2.91-2.950.27573930.251872387631100
2.95-30.30254050.262271347539100
3-3.060.27963910.248372047595100
3.06-3.120.28623610.241672227583100
3.12-3.180.26383870.22027148753599
3.18-3.250.2493830.21577235761899
3.25-3.330.24493430.211172357578100
3.33-3.410.2453680.209672077575100
3.41-3.50.24443260.211573037629100
3.5-3.60.24393840.20272097593100
3.6-3.720.2143850.190771637548100
3.72-3.850.20074180.173372567674100
3.85-4.010.20334340.166871327566100
4.01-4.190.19483720.168272597631100
4.19-4.410.17123800.15672257605100
4.41-4.690.18064000.153772317631100
4.69-5.050.18964030.15997199760299
5.05-5.560.18023960.164972497645100
5.56-6.360.21244070.179572457652100
6.36-8.010.20133500.171973417691100
8.01-48.840.17293230.1597002732594

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