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- PDB-2jlu: Dengue virus 4 NS3 helicase in complex with ssRNA -

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Basic information

Entry
Database: PDB / ID: 2jlu
TitleDengue virus 4 NS3 helicase in complex with ssRNA
Components
  • 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
  • SERINE PROTEASE SUBUNIT NS3
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / RIBONUCLEOPROTEIN / NUCLEOTIDE-BINDING / VIRAL NUCLEOPROTEIN / ENDOPLASMIC RETICULUM / HELICASE / PROTEASE / HYDROLASE / TRANSFERASE / CLEAVAGE ON PAIR OF BASIC RESIDUES / MULTIFUNCTIONAL ENZYME / TRANSCRIPTION REGULATION / NUCLEOTIDYLTRANSFERASE / NS3 HELICASE STRUCTURE / VIRION / ATPASE / NUCLEUS / MEMBRANE / SECRETED / ATP-BINDING / RNA-BINDING / FLAVIVIRUSES / GLYCOPROTEIN / RNA-DIRECTED RNA POLYMERASE / RNA REPLICATION / SERINE PROTEASE / ENVELOPE PROTEIN / DENGUE VIRUS / METAL-BINDING / TRANSMEMBRANE / TRANSCRIPTION / PHOSPHOPROTEIN / CAPSID PROTEIN
Function / homology
Function and homology information


flavivirin / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / ATP hydrolysis 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 / P-loop containing nucleotide triphosphate hydrolases / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 4
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLuo, D.H. / Xu, T. / Watson, R.P. / Becker, D.S. / Sampath, A. / Jahnke, W. / Yeong, S.S. / Wang, C.H. / Lim, S.P. / Vasudevan, S.G. / Lescar, J.
CitationJournal: Embo J. / Year: 2008
Title: Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein.
Authors: Luo, D. / Xu, T. / Watson, R.P. / Scherer-Becker, D. / Sampath, A. / Jahnke, W. / Yeong, S.S. / Wang, C.H. / Lim, S.P. / Strongin, A. / Vasudevan, S.G. / Lescar, J.
History
DepositionSep 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE PROTEASE SUBUNIT NS3
B: SERINE PROTEASE SUBUNIT NS3
C: 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
D: 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7068
Polymers110,3384
Non-polymers3684
Water7,332407
1
A: SERINE PROTEASE SUBUNIT NS3
C: 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2613
Polymers55,1692
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-4.1 kcal/mol
Surface area25230 Å2
MethodPQS
2
B: SERINE PROTEASE SUBUNIT NS3
D: 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4455
Polymers55,1692
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-3.1 kcal/mol
Surface area24990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.033, 105.497, 72.517
Angle α, β, γ (deg.)90.00, 117.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Refine code: 2

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLEULEUAA175 - 2708 - 103
211ASPASPLEULEUBB175 - 2708 - 103
121LEULEULYSLYSAA280 - 618113 - 451
221LEULEULYSLYSBB280 - 618113 - 451
112AAUUCC1 - 51 - 5
212AAUUDD1 - 51 - 5

NCS ensembles :
ID
1
2

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Components

#1: Protein SERINE PROTEASE SUBUNIT NS3 / DENV4 NS3 HELICASE / NON-STRUCTURAL PROTEIN 3


Mass: 51365.527 Da / Num. of mol.: 2 / Fragment: RESIDUES 1646-2092
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 4 / Strain: THAILAND/0348/1991 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2YHF0, flavivirin
#2: RNA chain 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'


Mass: 3803.360 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 38.81 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.8 Å / Num. obs: 54798 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.2 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JLQ

2jlq


Resolution: 2.04→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.489 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24198 2779 5.1 %RANDOM
Rwork0.19707 ---
obs0.19935 51971 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.244 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20.5 Å2
2---0.86 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 256 24 407 7895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227674
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3292.01210439
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86222.853347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.922151299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8381581
X-RAY DIFFRACTIONr_chiral_restr0.0920.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025743
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23416
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.25138
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2790.2463
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.2171
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6351.54649
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08327326
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52233497
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4454.53113
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1732tight positional0.060.05
1A1742medium positional0.570.5
2C104medium positional0.140.5
1A1732tight thermal0.090.5
1A1742medium thermal0.522
2C104medium thermal0.452
LS refinement shellResolution: 2.04→2.092 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 198
Rwork0.226 3582
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.16960.09070.25672.16020.36251.06550.0128-0.0648-0.14610.1570.0185-0.07350.2484-0.0571-0.03130.0079-0.0066-0.0012-0.08120.006-0.096639.7632-15.61721.7064
22.57080.29730.95311.32010.0971.7516-0.0796-0.10320.1782-0.01260.08310.3848-0.0062-0.2858-0.0035-0.06660.0147-0.004-0.06730.0105-0.033423.66174.8298-3.0308
30.7999-0.1766-0.24342.44171.49791.8341-0.0469-0.02570.02880.24310.1017-0.14030.15280.0809-0.0548-0.0650.0172-0.0189-0.0729-0.0081-0.072948.58411.172812.3141
41.6271-1.38870.310511.7407-4.40881.686-0.2684-0.23540.11950.42740.1462-0.3647-0.116-0.01620.12220.03410.03070.0089-0.01280.0125-0.023137.09080.549210.3491
51.2-0.3890.2962.4250.29350.63180.04560.12930.2858-0.0901-0.0155-0.1986-0.05550.013-0.0301-0.0818-0.01730.059-0.04760.0158-0.000221.5012-5.464336.4761
62.69620.31370.47890.57740.1660.79620.02280.2945-0.0588-0.16460.06010.1694-0.02190.0096-0.0829-0.0616-0.0015-0.001-0.0247-0.0143-0.06128.1716-25.792725.9748
71.3166-1.1857-0.40462.36040.83241.57180.0557-0.05730.1105-0.00720.0996-0.2732-0.05510.164-0.1553-0.0735-0.0160.0067-0.0476-0.0153-0.050435.007-32.403137.4018
80.9673.7196-0.01114.79760.43630.46690.12620.065-0.3255-0.120.0343-0.7877-0.04020.2201-0.16050.0008-0.02020.04080.0171-0.01-0.002226.7757-21.63929.1317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A168 - 326
2X-RAY DIFFRACTION2A327 - 481
3X-RAY DIFFRACTION3A482 - 618
4X-RAY DIFFRACTION4C1 - 7
5X-RAY DIFFRACTION5B168 - 326
6X-RAY DIFFRACTION6B327 - 481
7X-RAY DIFFRACTION7B482 - 618
8X-RAY DIFFRACTION8D1 - 7

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