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- PDB-2jlv: Dengue virus 4 NS3 helicase in complex with ssRNA and AMPPNP -

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Basic information

Entry
Database: PDB / ID: 2jlv
TitleDengue virus 4 NS3 helicase in complex with ssRNA and AMPPNP
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 / HELICASE / PROTEASE / HYDROLASE / ATP ANALOG / TRANSFERASE / VIRAL NUCLEOPROTEIN / ENDOPLASMIC RETICULUM / CLEAVAGE ON PAIR OF BASIC RESIDUES / SSRNA / VIRION / ATPASE / NUCLEUS / MEMBRANE / SECRETED / MULTIFUNCTIONAL ENZYME / TRANSCRIPTION REGULATION / NUCLEOTIDYLTRANSFERASE / NS3 HELICASE STRUCTURE / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
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 capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...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. / 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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 4
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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)111,71512
Polymers110,3384
Non-polymers1,3778
Water12,899716
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)55,8586
Polymers55,1692
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-3.2 kcal/mol
Surface area24800 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)55,8586
Polymers55,1692
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-3.4 kcal/mol
Surface area24720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)132.660, 105.192, 72.435
Angle α, β, γ (deg.)90.00, 117.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 724 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 1.98 Å3/Da / Density % sol: 37.4 % / 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: 2.3→2.4 Å / Num. obs: 44454 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 98.6

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Processing

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

2jlu


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.948 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24801 3105 5.1 %RANDOM
Rwork0.19049 ---
obs0.19349 57632 87.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.077 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20.6 Å2
2---1.11 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7218 256 78 716 8268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227768
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3382.0210584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69622.816348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.108151312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5881582
X-RAY DIFFRACTIONr_chiral_restr0.0930.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025794
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.23611
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.25150
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2654
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.2155
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.54666
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94127364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.35433594
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1534.53220
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
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 177 -
Rwork0.25 3238 -
obs--67.26 %
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)
11.78810.27340.96162.3346-0.24641.41240.00380.0625-0.138-0.14170.04810.04060.20970.0403-0.0519-0.01320.0032-0.0137-0.1082-0.0091-0.12499.2338-15.052330.3533
21.69010.04211.05981.19520.10771.3712-0.12030.16040.10510.05720.0718-0.2776-0.13040.30020.0486-0.0458-0.0359-0.0457-0.03790.0143-0.06625.47075.03735.3054
30.74650.4462-0.543.0888-1.97711.9623-0.04060.07660.0084-0.28190.14480.23050.1963-0.1148-0.1042-0.0602-0.0289-0.0637-0.06960.013-0.04550.553811.784319.9547
41.54435.00981.620826.16295.49892.2971-0.30710.31040.3023-1.09720.08720.7262-0.19620.20860.21980.03790.0031-0.0339-0.01890.0061-0.088612.06310.966521.6332
52.11720.54190.58642.4089-0.4341.13470.0739-0.10580.39690.08130.00240.3351-0.1794-0.0894-0.0763-0.05110.01340.0606-0.0913-0.01360.032527.9042-4.7669-4.3603
63.11070.12250.24170.7396-0.12020.67850.0625-0.405-0.14080.14090.027-0.19870.01060.0773-0.0895-0.0892-0.0192-0.01-0.01970.0278-0.053441.3477-24.84876.0046
71.59391.0948-0.39492.8496-1.16432.01520.0040.07910.168-0.08370.09810.2799-0.0724-0.1363-0.1021-0.08240.0149-0.0335-0.06650.006-0.058114.325-31.6055-5.4471
83.552-8.95362.807731.0036-4.24723.1691-0.22-0.4253-0.7980.73540.23922.07630.1182-0.4465-0.0192-0.1225-0.03610.07140.0368-0.04830.068622.5712-20.79693.1383
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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