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- PDB-2jlw: Dengue virus 4 NS3 helicase in complex with ssRNA2 -

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Basic information

Entry
Database: PDB / ID: 2jlw
TitleDengue virus 4 NS3 helicase in complex with ssRNA2
Components
  • 5'-R(*UP*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
  • SERINE PROTEASE SUBUNIT NS3
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / RNA-BINDING / FLAVIVIRUSES / GLYCOPROTEIN / DENGUE VIRUS / TRANSCRIPTION REGULATION / RNA-DIRECTED RNA POLYMERASE / NUCLEOTIDE-BINDING / VIRAL NUCLEOPROTEIN / CLEAVAGE ON PAIR OF BASIC RESIDUES / PROTEASE / HYDROLASE / TRANSFERASE / ATP-BINDING / ENDOPLASMIC RETICULUM / NUCLEOTIDYLTRANSFERASE / PHOSPHOPROTEIN / CAPSID PROTEIN / RNA REPLICATION / SERINE PROTEASE / ENVELOPE PROTEIN / RIBONUCLEOPROTEIN / NS3 HELICASE STRUCTURE / MULTIFUNCTIONAL ENZYME / SSRNA / VIRION / NUCLEUS / MEMBRANE / SECRETED / HELICASE / METAL-BINDING / TRANSMEMBRANE / TRANSCRIPTION
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
PHOSPHATE ION / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 4
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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.H. / Xu, T. / Watson, R.P. / Becker, D.S. / 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(*UP*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
D: 5'-R(*UP*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2327
Polymers110,9504
Non-polymers2823
Water2,324129
1
A: SERINE PROTEASE SUBUNIT NS3
C: 5'-R(*UP*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5703
Polymers55,4752
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-2.8 kcal/mol
Surface area25420 Å2
MethodPQS
2
B: SERINE PROTEASE SUBUNIT NS3
D: 5'-R(*UP*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6624
Polymers55,4752
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-5.3 kcal/mol
Surface area25110 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.432, 104.628, 72.317
Angle α, β, γ (deg.)90.00, 117.67, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14C
24D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPRO2AA168 - 3261 - 159
21GLYGLYPROPRO2BB168 - 3261 - 159
12GLNGLNASNASN2AA327 - 481160 - 314
22GLNGLNASNASN2BB327 - 481160 - 314
13ASPASPLYSLYS2AA482 - 618315 - 451
23ASPASPLYSLYS2BB482 - 618315 - 451
14UUAA1CC1 - 71 - 7
24UUAA1DD1 - 71 - 7

NCS ensembles :
ID
1
2
3
4

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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(*UP*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'


Mass: 4109.525 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.1 Å3/Da / Density % sol: 40.8 % / 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: 2.6→43.4 Å / Num. obs: 26932 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

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

2jlq


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.881 / SU B: 29.059 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27007 1348 5 %RANDOM
Rwork0.19872 ---
obs0.20236 25521 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.22 Å2
2---0.42 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 256 16 129 7564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2122.01210371
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.375894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79322.945343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.614151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6021578
X-RAY DIFFRACTIONr_chiral_restr0.0750.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.23327
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25120
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2120
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3781.54606
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64527284
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.80233471
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3934.53087
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A632tight positional0.030.05
12B632tight positional0.030.05
21A616tight positional0.030.05
22B616tight positional0.030.05
31A532tight positional0.040.05
32B532tight positional0.040.05
41C128tight positional0.120.05
42D128tight positional0.120.05
11A588medium positional0.460.5
12B588medium positional0.460.5
21A608medium positional0.440.5
22B608medium positional0.440.5
31A572medium positional0.490.5
32B572medium positional0.490.5
11A632tight thermal0.040.5
12B632tight thermal0.040.5
21A616tight thermal0.040.5
22B616tight thermal0.040.5
31A532tight thermal0.070.5
32B532tight thermal0.070.5
41C128tight thermal0.040.5
42D128tight thermal0.040.5
11A588medium thermal0.292
12B588medium thermal0.292
21A608medium thermal0.272
22B608medium thermal0.272
31A572medium thermal0.352
32B572medium thermal0.352
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 82
Rwork0.283 1876
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)
13.28710.34031.04053.0994-0.0551.19890.00620.0357-0.1237-0.0850.0145-0.01440.25610.0651-0.02070.02710.00310.0096-0.0756-0.0138-0.1132-39.9544-5.2009-1.5662
24.1412-0.53531.60221.04810.10861.85010.03390.23230.22290.11550.0095-0.3918-0.06040.2788-0.0434-0.0124-0.0568-0.0213-0.0292-0.0054-0.0586-23.580814.8263.2603
31.17321.0031-0.98374.5374-2.80513.3755-0.02780.08360.0058-0.12930.11620.10560.0471-0.1333-0.0884-0.11340.0145-0.0332-0.062-0.0195-0.0366-48.777921.6466-12.2346
411.45150.98642.917416.0173-1.20820.8769-0.52490.65310.6884-0.24770.23971.01530.1091-0.29020.2851-0.0159-0.0574-0.0647-0.0290.0753-0.0319-36.515312.0576-11.1895
51.43120.1540.58092.9886-0.55191.91130.1328-0.04520.2070.2062-0.00390.174-0.1673-0.0678-0.1289-0.04050.01440.0617-0.04630.00380.0017-21.45495.2859-36.3312
64.78720.22780.55410.41270.14811.34810.0144-0.4256-0.03190.05510.0824-0.13440.04430.0415-0.0968-0.06750.0489-0.0017-0.03870.0628-0.0429-8.1621-14.7401-25.7686
71.60431.7004-0.02684.6749-1.61012.0786-0.03180.13040.0384-0.10490.1460.29020.0148-0.1572-0.1142-0.07950.0353-0.0247-0.01970.0125-0.0394-35.2276-21.8046-37.2493
819.1134-4.551.99431.9191-3.94033.20820.07290.351-0.4629-0.3341-0.13881.65150.2043-0.10750.0659-0.0513-0.0251-0.0481-0.03990.0689-0.121-27.2974-11.968-28.1029
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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