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- PDB-3p54: Crystal Structure of the Japanese Encephalitis Virus Envelope Pro... -

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Basic information

Entry
Database: PDB / ID: 3p54
TitleCrystal Structure of the Japanese Encephalitis Virus Envelope Protein, strain SA-14-14-2.
Componentsenvelope glycoprotein
KeywordsVIRAL PROTEIN / Viral envelope proteins / structural genomics / fusion peptide / antibody epitopes / Flavivirus / Japanese Encephalitis Virus / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / host cell surface / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / 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 / endoplasmic reticulum membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / nucleus / metal ion binding
Similarity search - Function
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / : / Flavivirus capsid protein C superfamily / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus non-structural protein NS2B / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / 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, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 / 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 / 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 / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Core protein
Similarity search - Component
Biological speciesJapanese encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.097 Å
AuthorsLuca, V.C. / Nelson, C.A. / AbiMansour, J.P. / Diamond, M.S. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Virol. / Year: 2012
Title: Crystal structure of the Japanese encephalitis virus envelope protein.
Authors: Luca, V.C. / Abimansour, J. / Nelson, C.A. / Fremont, D.H.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
Revision 1.3Feb 8, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)43,6861
Polymers43,6861
Non-polymers00
Water3,783210
1
A: envelope glycoprotein

A: envelope glycoprotein

A: envelope glycoprotein

A: envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)174,7454
Polymers174,7454
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5730 Å2
ΔGint-47 kcal/mol
Surface area72320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.111, 62.398, 243.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein envelope glycoprotein


Mass: 43686.277 Da / Num. of mol.: 1 / Fragment: JEV Envelope residues 295-700
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Japanese encephalitis virus / Strain: SA-14-14-2 / Gene: Envelope protein E / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q99DQ9, UniProt: P27395*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 3350, 0.2M Sodium citrate, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 / Detector: CCD / Date: Aug 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 15.16 / Number: 115887 / Rmerge(I) obs: 0.07 / Χ2: 1.05 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 26920 / % possible obs: 96.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525098.710.0311.054.6
3.594.5292.310.0580.9924.2
3.143.5999.810.061.0314.4
2.853.1499.110.0711.0654.3
2.652.8598.210.1011.0984.3
2.492.659810.1451.0744.3
2.372.4997.610.2081.024.4
2.262.379510.2791.0384.2
2.182.2693.610.3261.0353.9
2.12.1896.910.4271.0614.4
ReflectionResolution: 2.097→50 Å / Num. all: 27776 / Num. obs: 26920 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Χ2: 1.047 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.097-2.184.40.42726501.061196.9
2.18-2.263.90.32625381.035193.6
2.26-2.374.20.27926091.038195
2.37-2.494.40.20826671.02197.6
2.49-2.654.30.14526971.074198
2.65-2.854.30.10127081.098198.2
2.85-3.144.30.07127601.065199.1
3.14-3.594.40.0627721.031199.8
3.59-4.524.20.05825950.992192.3
4.52-504.60.03129241.05198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å30.19 Å
Translation4 Å30.19 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.097→30.188 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8662 / SU ML: 0.23 / σ(F): 0.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 1284 5 %RANDOM
Rwork0.1788 ---
all0.1811 27776 --
obs0.1811 25663 92.24 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.732 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso max: 162.61 Å2 / Biso mean: 54.6726 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.5614 Å2-0 Å2-0 Å2
2--1.0597 Å2-0 Å2
3----0.4982 Å2
Refinement stepCycle: LAST / Resolution: 2.097→30.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 210 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093117
X-RAY DIFFRACTIONf_angle_d1.0984218
X-RAY DIFFRACTIONf_chiral_restr0.074475
X-RAY DIFFRACTIONf_plane_restr0.005543
X-RAY DIFFRACTIONf_dihedral_angle_d11.7321104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0971-2.18110.22941360.20372470260686
2.1811-2.28030.34431160.25692220233677
2.2803-2.40050.2491410.20462621276290
2.4005-2.55080.21491400.18352722286294
2.5508-2.74760.22561470.17642775292295
2.7476-3.02390.24971480.18682840298897
3.0239-3.46090.21961500.18322907305799
3.4609-4.35830.22371460.16012752289893
4.3583-30.19090.18791600.16213072323299
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)
12.89770.0074-0.43663.53120.18050.0893-0.2192-0.7063-0.16391.192-0.2984-0.0094-0.05140.3450.33280.432-0.00670.05240.36230.12050.1996-16.2651-20.0399-40.0904
20.4459-0.0847-1.0833.13921.09522.90810.08310.084-0.41060.3112-0.5740.83960.79080.31070.59130.42330.0340.1330.38350.07310.3075-23.0534-8.896-39.8521
31.65811.3292-2.26394.8706-1.22393.15880.20990.0493-0.01190.7030.21740.8033-0.036-0.178-0.27410.2330.00250.06060.1120.02920.1601-17.4587-11.7127-45.1385
4-0.6735-0.1645-0.4056-0.4069-1.30787.52950.10790.2068-0.0949-0.1224-0.25420.0331-1.48690.47550.17620.993-0.0737-0.02080.67110.1620.2287-8.3797-18.977616.8508
52.929-0.44440.54253.6651.16271.2274-0.1267-0.9437-0.02471.16930.394-0.34150.00730.2481-0.07340.59660.0739-0.07640.37860.04360.1529-9.7301-10.6934-35.0075
62.5465-0.41321.24913.0829-1.46051.3026-0.1158-0.41170.27431.16360.3465-0.6869-0.4290.1244-0.03120.46170.0289-0.06460.2864-0.04870.0843-8.665-5.9465-39.0664
70.6988-1.3016-0.0514.88930.76110.1887-0.1245-0.5562-0.0128-0.37110.5879-0.3571-0.1589-0.829-0.14661.36430.33390.05151.6079-0.15210.9064-20.9853-6.4614-17.5157
81.1411-0.9268-0.21581.30380.14890.0643-0.06540.14890.046-0.4816-0.2474-0.2891.31310.5980.34241.59440.4010.0060.79780.09890.1946-12.4807-17.9377-9.5814
90.54020.9702-1.18032.9836-3.90095.11120.4086-0.1040.04081.4783-0.10450.5619-1.42640.4125-0.24190.9750.10440.08340.52240.00020.2094-16.0272-12.71442.1295
100.31220.13230.46971.1748-0.34330.9010.1959-0.0514-0.24690.1244-0.49010.02520.38980.58050.47010.94890.00950.02820.71430.02190.1534-10.932-26.543412.7128
110.4720.08430.10471.3687-0.28370.08470.1320.24930.0403-0.6595-0.45850.02020.00210.37820.29511.47540.1399-0.00460.9806-0.07810.2481-10.9472-17.5718-14.6068
124.2085-1.6873-3.16362.39511.3772.382-0.29610.2549-0.16062.00580.44910.16040.5666-0.7120.03892.16970.20880.44430.76230.01360.5798-16.0857-13.8743-23.1003
130.9277-0.4-1.53940.4461.12373.29730.1414-0.07010.29450.10540.2146-0.1771-0.332-0.0158-0.28240.20030.07470.00470.1002-0.00440.1967-15.2492-4.1821-48.2292
140.18140.35350.10421.09460.13920.9046-0.03650.1567-0.2726-0.1519-0.29310.06730.00920.03820.25070.09110.01640.020.1094-0.03320.1726-5.8754-20.0506-67.921
150.148-0.2329-0.13551.9535-0.06630.79870.0514-0.02780.0410.0042-0.062-0.112-0.00270.01050.00630.0304-0.0098-0.00280.04040.0160.1139-13.5023-22.8521-58.7873
164.43861.4869-2.43091.7441-0.71642.39770.29150.4357-0.6561-0.5284-0.67630.0037-0.1024-0.19730.2871-0.161-0.2254-0.0768-0.0029-0.07490.1384-19.7602-30.9191-60.2372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:12)A1 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:29)A13 - 29
3X-RAY DIFFRACTION3(chain A and resid 30:44)A30 - 44
4X-RAY DIFFRACTION4(chain A and resid 45:130)A45 - 130
5X-RAY DIFFRACTION5(chain A and resid 131:150)A131 - 150
6X-RAY DIFFRACTION6(chain A and resid 151:192)A151 - 192
7X-RAY DIFFRACTION7(chain A and resid 193:201)A193 - 201
8X-RAY DIFFRACTION8(chain A and resid 202:213)A202 - 213
9X-RAY DIFFRACTION9(chain A and resid 214:234)A214 - 234
10X-RAY DIFFRACTION10(chain A and resid 235:265)A235 - 265
11X-RAY DIFFRACTION11(chain A and resid 266:278)A266 - 278
12X-RAY DIFFRACTION12(chain A and resid 279:284)A279 - 284
13X-RAY DIFFRACTION13(chain A and resid 285:302)A285 - 302
14X-RAY DIFFRACTION14(chain A and resid 303:308)A303 - 308
15X-RAY DIFFRACTION15(chain A and resid 309:386)A309 - 386
16X-RAY DIFFRACTION16(chain A and resid 387:404)A387 - 404

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