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- PDB-2whx: A second conformation of the NS3 protease-helicase from dengue virus -

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Basic information

Entry
Database: PDB / ID: 2whx
TitleA second conformation of the NS3 protease-helicase from dengue virus
Components
  • SERINE PROTEASE SUBUNIT NS2B
  • SERINE PROTEASE/NTPASE/HELICASE NS3
KeywordsHYDROLASE / TRANSCRIPTION / ATP-BINDING / RETICULUM / NUCLEOTIDYLTRANSFERASE / MULTIFUNCTIONAL ENZYME / TRANSCRIPTION REGULATION / RIBONUCLEOPROTEIN / RNA-DIRECTED RNA POLYMERASE / RNA REPLICATION / ENVELOPE 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
Thrombin, subunit H - #120 / 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 ...Thrombin, subunit H - #120 / 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 / Thrombin, subunit H / 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 / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 4
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsLuo, D. / Lescar, J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Flexibility between the Protease and Helicase Domains of the Dengue Virus Ns3 Protein Conferred by the Linker Region and its Functional Implications.
Authors: Luo, D. / Wei, N. / Doan, D.N. / Paradkar, P.N. / Chong, Y. / Davidson, A.D. / Kotaka, M. / Lescar, J. / Vasudevan, S.G.
History
DepositionMay 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE PROTEASE/NTPASE/HELICASE NS3
C: SERINE PROTEASE SUBUNIT NS2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6036
Polymers71,0502
Non-polymers5534
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-51.1 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 87.720, 75.779
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein SERINE PROTEASE/NTPASE/HELICASE NS3 / THE NS3 PROTEASE-HELICASE FROM DENGUE VIRUS / NON-STRUCTURAL PROTEIN 3 / SERINE PROTEASE SUBUNIT ...THE NS3 PROTEASE-HELICASE FROM DENGUE VIRUS / NON-STRUCTURAL PROTEIN 3 / SERINE PROTEASE SUBUNIT NS3 / SERINE PROTEASE SUBUNIT NS3 / NON-STRUCTURAL PROTEIN 3


Mass: 69489.172 Da / Num. of mol.: 1 / Fragment: RESIDUES 1475-2092
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 4 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q2YHF0, flavivirin, nucleoside-triphosphate phosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide SERINE PROTEASE SUBUNIT NS2B / THE NS3 PROTEASE-HELICASE FROM DENGUE VIRUS / NON-STRUCTURAL PROTEIN 2B / FLAVIVIRIN PROTEASE NS2B ...THE NS3 PROTEASE-HELICASE FROM DENGUE VIRUS / NON-STRUCTURAL PROTEIN 2B / FLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT


Mass: 1560.683 Da / Num. of mol.: 1 / Fragment: RESIDUES 1393-1406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DENGUE VIRUS 4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2YHF0

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Non-polymers , 4 types, 141 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.56 Å3/Da / Density % sol: 51.53 % / Description: NONE
Crystal growpH: 7.4 / Details: pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Type: NSRRC / Wavelength: 0.97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 31361 / % possible obs: 90.4 % / Observed criterion σ(I): 2.2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.5

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Processing

SoftwareName: REFMAC / Version: 5.5.0072 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.2→19.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.322 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27233 1555 5 %RANDOM
Rwork0.22806 ---
obs0.23031 29746 90.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å2-0.17 Å2
2---0.21 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 30 137 4860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9646542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23922.982218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32315822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5121547
X-RAY DIFFRACTIONr_chiral_restr0.0780.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213665
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2911.52965
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55624787
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.84131861
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3824.51755
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: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 69 -
Rwork0.28 1365 -
obs--56.52 %
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)
15.08954.43871.988810.01052.72153.19520.3608-0.0641-0.34791.2347-0.1693-1.15110.24870.22-0.19150.5733-0.0551-0.15480.47790.12120.43885.83569.4345-7.7627
25.2221-0.44670.71561.8758-0.76621.3373-0.03130.64450.1377-0.2674-0.0499-0.2389-0.00980.27860.08110.09-0.00260.05710.16850.02460.044834.41373.977920.5006
32.94770.42390.96382.446-0.44522.19470.0842-0.0453-0.23190.03080.05320.13050.1212-0.0488-0.13740.03840.02620.02550.05250.01670.081911.6265-9.160728.9083
41.62881.9082-0.79087.8313-3.01072.77190.1585-0.136-0.35950.1199-0.3071-0.37320.08690.21470.14860.0835-0.0065-0.01370.11890.00450.094233.6481-5.554246.3241
511.545411.6936-1.687614.4932-1.26291.53610.5251-0.69930.51821.3049-0.72310.3494-0.2497-0.14970.19790.7662-0.07030.03220.5996-0.01220.4419-2.285214.7626-4.0524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 179
2X-RAY DIFFRACTION2A180 - 316
3X-RAY DIFFRACTION3A317 - 481
4X-RAY DIFFRACTION4A482 - 618
5X-RAY DIFFRACTION5C49 - 62

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