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- PDB-4r8t: Structure of JEV protease -

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Basic information

Entry
Database: PDB / ID: 4r8t
TitleStructure of JEV protease
Components
  • NS3
  • Serine protease subunit NS2B
KeywordsHYDROLASE / Serine protease / Protease / NS2b
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / endoplasmic reticulum membrane / virion attachment to host cell / virion membrane / structural molecule activity / extracellular region / ATP binding / metal ion binding / nucleus
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 / Flavivirus capsid protein C ...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. / 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 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Core protein / Genome polyprotein
Similarity search - Component
Biological speciesJapanese encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.133 Å
AuthorsNair, D.T. / Weinert, T. / Wang, M. / Olieric, V.
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionSep 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references / Experimental preparation
Revision 1.2Jan 14, 2015Group: Structure summary
Revision 1.3Aug 12, 2015Group: Database references
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 subunit NS2B
B: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6873
Polymers17,6522
Non-polymers351
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-27 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.260, 88.260, 36.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein/peptide Serine protease subunit NS2B /


Mass: 2501.765 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1352-1368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus / Strain: Nakayama / Gene: NS3 / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P14403
#2: Protein NS3


Mass: 15150.038 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1522-1662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Japanese encephalitis virus / Gene: NS3 / Production host: Escherichia coli (E. coli) / References: UniProt: O90417
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 25% PEG 1000, 0.1M Citrate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 18, 2014
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.133→44.13 Å / Num. all: 9029 / Num. obs: 9129 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.133→2.2453 Å / % possible all: 99

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.133→44.13 Å / SU ML: 0.23 / σ(F): 1.41 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 912 10.1 %random
Rwork0.1642 ---
obs0.1697 9029 98.31 %-
all-9029 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.133→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 0 1 104 1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031259
X-RAY DIFFRACTIONf_angle_d0.7081712
X-RAY DIFFRACTIONf_dihedral_angle_d11.129441
X-RAY DIFFRACTIONf_chiral_restr0.031184
X-RAY DIFFRACTIONf_plane_restr0.002221
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1329-2.24530.21961130.1645102388
2.2453-2.3860.23421310.171184100
2.386-2.57020.23781290.17571163100
2.5702-2.82880.24781310.18051161100
2.8288-3.23810.23911310.17861184100
3.2381-4.07920.20041380.15211178100
4.0792-44.13940.19171390.15171224100
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)
12.15710.30591.09312.96670.14812.34920.0391-0.04750.51660.1047-0.0701-0.2258-0.2330.126-0.02010.143-0.01870.0020.09720.02480.0507-13.3192-12.2758.4197
26.54753.0132.19665.80654.94294.2662-0.13320.74470.6933-0.2466-0.44410.7629-0.42480.2203-0.13070.30070.0122-0.10060.27030.05180.5421-34.733-14.3954-2.3485
31.6643-0.6578-0.81492.212-0.8412.5125-0.0316-0.28010.56550.00310.0343-0.2687-0.15730.3116-0.22470.1042-0.0036-0.05420.1424-0.01330.1681-10.9023-12.79148.0393
42.6285-0.08770.36261.9027-0.97542.6744-0.05440.03710.0210.0852-0.00730.0522-0.06540.08890.00250.1109-0.0007-0.01620.08090.00040.0992-14.0558-18.747711.7936
54.63860.88650.32640.9811-0.35866.10860.18310.21651.02350.23860.0037-0.2643-0.91890.28150.34560.2386-0.0726-0.0160.16790.01830.2873-6.8831-13.956216.9728
63.2109-0.8775-0.49742.25810.38853.72450.0253-0.1003-0.45950.36460.20750.15760.5459-0.07190.03370.1678-0.0252-0.02050.12790.02720.1274-14.1238-26.540718.6185
72.73460.4012.98352.4571.51884.06160.1349-0.4202-0.28330.0134-0.08160.55570.1628-0.59-0.22540.1523-0.0356-0.01560.20.07510.1747-29.0827-25.417913.9332
83.39360.69720.09412.1881-0.53350.87070.01070.26220.0842-0.08120.0421-0.04060.18260.0026-0.04420.10620.0171-0.0340.14310.00470.0918-21.3245-17.1459-0.2986
90.5326-0.3363-0.07064.1343-1.10990.36440.15690.2998-0.2-0.3190.24390.1010.7083-0.26320.29910.4065-0.0856-0.17350.14620.01420.2189-29.1879-27.52811.1043
101.5804-0.1199-0.9831.8174-1.80962.4679-0.24070.082-0.2533-0.69650.13240.50520.3349-0.2622-0.4980.3936-0.0205-0.10920.1184-0.02760.2172-22.9721-32.67933.9104
113.3183-2.464-0.54552.3634-0.52465.01740.26630.1670.0819-0.07460.0143-0.5890.52840.6634-0.08920.14730.0182-0.03480.1549-0.05430.1976-14.4786-21.95632.8825
122.4743-0.65990.33154.47820.58172.48580.1085-0.2432-0.28560.05-0.02610.51030.0769-0.3909-0.05590.1453-0.0181-0.04080.15240.02880.1895-28.0602-25.16099.7684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 48 THROUGH 62 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 63 THROUGH 68 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 18 THROUGH 31 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 32 THROUGH 53 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 54 THROUGH 66 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 67 THROUGH 79 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 80 THROUGH 94 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 95 THROUGH 106 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 107 THROUGH 117 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 118 THROUGH 131 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 132 THROUGH 137 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 138 THROUGH 158 )

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