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- PDB-5k5m: Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA... -

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Basic information

Entry
Database: PDB / ID: 5k5m
TitleCo-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27
ComponentsRNA Dependent RNA PolymeraseRNA-dependent RNA polymerase
KeywordsHYDROLASE / RNA Dependent RNA Polymerase / Dengue
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 / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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 RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 / Alpha-Beta Plaits / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-68T / Core protein / Core protein
Similarity search - Component
Biological speciesDengue virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å
AuthorsArora, R. / Benson, T.E.
CitationJournal: Plos Pathog. / Year: 2016
Title: Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling.
Authors: Lim, S.P. / Noble, C.G. / Seh, C.C. / Soh, T.S. / El Sahili, A. / Chan, G.K. / Lescar, J. / Arora, R. / Benson, T. / Nilar, S. / Manjunatha, U. / Wan, K.F. / Dong, H. / Xie, X. / Shi, P.Y. / Yokokawa, F.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA Dependent RNA Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5905
Polymers73,7771
Non-polymers8144
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint1 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.140, 115.770, 148.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1004-

MES

21A-1108-

HOH

31A-1150-

HOH

41A-1174-

HOH

51A-1504-

HOH

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Components

#1: Protein RNA Dependent RNA Polymerase / RNA-dependent RNA polymerase


Mass: 73776.891 Da / Num. of mol.: 1 / Fragment: UNP Residues 2757-3391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: B5LNH6, UniProt: A0A097PIE2*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-68T / 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-[(3-methoxyphenyl)sulfonyl]benzamide


Mass: 487.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21NO7S2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.62 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 0.35M MgCl2, 16% PEG 4000, 0.1M MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→91.32 Å / Num. obs: 47145 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Net I/σ(I): 24.3
Reflection shellResolution: 2.01→2.02 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 3.74 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 2.01→91.32 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9238 / SU R Cruickshank DPI: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2384 5.06 %RANDOM
Rwork0.1777 ---
obs0.1796 47141 99.34 %-
Displacement parametersBiso max: 145.17 Å2 / Biso mean: 44.9 Å2 / Biso min: 3.37 Å2
Baniso -1Baniso -2Baniso -3
1-9.6222 Å20 Å20 Å2
2---3.7945 Å20 Å2
3----5.8277 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 2.01→91.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 59 429 5120
Biso mean--35.96 44.67 -
Num. residues----563
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1748SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes712HARMONIC5
X-RAY DIFFRACTIONt_it4829HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion596SEMIHARMONIC5
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_contact5778SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4829HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6532HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion17.14
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2186 166 5.27 %
Rwork0.1991 2984 -
all0.2001 3150 -
obs--91.26 %

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