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- PDB-3n43: Crystal structures of the mature envelope glycoprotein complex (t... -

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Basic information

Entry
Database: PDB / ID: 3n43
TitleCrystal structures of the mature envelope glycoprotein complex (trypsin cleavage) of Chikungunya virus.
Components
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
  • E3 envelope glycoprotein
KeywordsVIRAL PROTEIN / IMMATURE HETERODIMER / ALPHAVIRUS / RECEPTOR BINDING / MEMBRANE FUSION
Function / homologyAlphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set ...Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Alphavirus E1 glycoprotein / togavirin / host cell membrane / viral capsid / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / identical protein binding / Togavirin
Function and homology information
Specimen sourceChikungunya virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.58 Å resolution
AuthorsVoss, J. / Vaney, M.C. / Duquerroy, S. / Rey, F.A.
Citation
Journal: Nature / Year: 2010
Title: Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography.
Authors: James E Voss / Marie-Christine Vaney / Stéphane Duquerroy / Clemens Vonrhein / Christine Girard-Blanc / Elodie Crublet / Andrew Thompson / Gérard Bricogne / Félix A Rey
#1: Journal: Structure / Year: 2006
Title: Structure and interactions at the viral surface of the envelope protein E1 of Semliki Forest virus.
Authors: Roussel, A. / Lescar, J. / Vaney, M.C. / Wengler, G. / Rey, F.A.
#2: Journal: Nature / Year: 2004
Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus.
Authors: Gibbons, D.L. / Vaney, M.C. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / Rey, F.A.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH.
Authors: Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Rey, F.A.
#4: Journal: To be Published
Title: Structural Changes of Envelope Proteins During Alphavirus Fusion.
Authors: Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 21, 2010 / Release: Dec 1, 2010
RevisionDateData content typeGroupProviderType
1.0Dec 1, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 envelope glycoprotein
B: E2 envelope glycoprotein
F: E1 envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1507
Polyers98,4283
Non-polymers7234
Water2,756153
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7810
ΔGint (kcal/M)-20
Surface area (Å2)37100
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)58.406, 90.812, 179.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 3 types, 3 molecules ABF

#1: Protein/peptide E3 envelope glycoprotein


Mass: 7470.737 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 268-318 / Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5
#2: Protein/peptide E2 envelope glycoprotein


Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 332-667 / Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5
#3: Protein/peptide E1 envelope glycoprotein


Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1200 / Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster (fruit fly) / References: UniProt: Q1H8W5

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Non-polymers , 4 types, 157 molecules

#4: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical ChemComp-NDG / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Formula: C2H3O2 / Acetate
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Formula: H2O / Water

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Details

Sequence detailsTHE RESIDUES ARE PART OF THE LINKER BETWEEN P AND F CHAINS. LINKER WAS CLEAVED BY CHYMOTRYPSIN ...THE RESIDUES ARE PART OF THE LINKER BETWEEN P AND F CHAINS. LINKER WAS CLEAVED BY CHYMOTRYPSIN BEFORE CRYSTALLIZATION.

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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: 2.42 / Density percent sol: 49.12 %
Crystal growTemp: 293 K / pH: 7
Details: 8-12% PEG4K, 100mM NaAcetate, 100mM Hepes pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID23-2 / Synchrotron site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD
Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
Detector: CCD / Collection date: Sep 19, 2009
RadiationMonochromator: SI(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 47.71 Å2 / D resolution high: 2.58 Å / D resolution low: 89.72 Å / Observed criterion sigma I: 0 / Rsym value: 0.129 / NetI over sigmaI: 8.8 / Redundancy: 3.9 % / Percent possible obs: 97.7
Reflection shellHighest resolution: 2.6 Å / Lowest resolution: 2.73 Å / MeanI over sigI obs: 2 / Rsym value: 0.31 / Redundancy: 2 % / Percent possible all: 93.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
RefineMethod to determine structure: SAD
Starting model: P62E1 ENVELOPE GLYCOPROTEINS FROM CHIKUNGUNYA VIRUS

Correlation coeff Fo to Fc: 0.867 / Correlation coeff Fo to Fc free: 0.862 / Overall SU R Cruickshank DPI: 0.693 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Displacement parametersB iso mean: 45.49 Å2 / Aniso B11: 0.5439 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 11.5921 Å2 / Aniso B23: 0 Å2 / Aniso B33: -12.136 Å2
Least-squares processR factor R free: 0.257 / R factor R work: 0.245 / R factor obs: 0.246 / Highest resolution: 2.58 Å / Lowest resolution: 44 Å / Number reflection R free: 1525 / Number reflection all: 35436 / Number reflection obs: 30189 / Percent reflection R free: 5.05 / Percent reflection obs: 97.8
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refine hist #LASTHighest resolution: 2.58 Å / Lowest resolution: 44 Å
Number of atoms included #LASTProtein: 6039 / Nucleic acid: 0 / Ligand: 46 / Solvent: 153 / Total: 6238
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076261HARMONIC2.000
X-RAY DIFFRACTIONt_angle_deg0.918545HARMONIC2.000
X-RAY DIFFRACTIONt_dihedral_angle_d2066SINUSOIDAL2.000
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes147HARMONIC2.000
X-RAY DIFFRACTIONt_gen_planes910HARMONIC5.000
X-RAY DIFFRACTIONt_it6261HARMONIC20.000
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.590
X-RAY DIFFRACTIONt_other_torsion17.960
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion842SEMIHARMONIC5.000
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6330SEMIHARMONIC4.000
Refine LS shellHighest resolution: 2.58 Å / R factor R free: 0.2536 / R factor R work: 0.2698 / R factor all: 0.2689 / Lowest resolution: 2.67 Å / Number reflection R free: 145 / Number reflection R work: 2323 / Number reflection all: 2468 / Total number of bins used: 15 / Percent reflection R free: 5.88 / Percent reflection obs: 97.78
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.2667-0.79231.08701.1776-0.70070.00000.00510.02830.0181-0.0293-0.01610.0400-0.0057-0.04010.0109-0.10700.0107-0.0979-0.00750.03900.1889-56.3158-13.8192-35.7624
22.03461.93890.41174.90021.51760.1571-0.0117-0.05400.08910.5497-0.13070.40310.0960-0.02660.14240.0498-0.05140.1550-0.2137-0.0112-0.1004-35.9239-15.9275-17.5114
37.22120.5172-1.42190.24030.66990.7213-0.00070.1029-0.1125-0.08480.0021-0.04610.1839-0.0084-0.0014-0.0922-0.11480.0136-0.06020.05460.0305-50.1099-45.3983-31.6891
43.0112-1.06221.68501.48032.52502.94730.0064-0.16960.01360.1867-0.0069-0.0692-0.00560.07150.0005-0.0331-0.0711-0.1466-0.11180.01210.0100-4.113513.2130-9.1537
50.49551.19860.21262.15200.13760.6653-0.01780.0914-0.0720-0.07540.00630.0603-0.0048-0.00590.0114-0.0485-0.0168-0.0164-0.03140.01700.0253-12.774536.1377-28.2726
60.06051.4476-0.72315.38821.42233.43890.02330.03960.0148-0.0655-0.0044-0.1009-0.1068-0.0101-0.0189-0.14810.0020-0.0477-0.07830.00240.0403-18.39781.4250-33.9163
71.59881.12921.10593.12691.15031.23250.0198-0.0535-0.0363-0.07100.01700.0516-0.0229-0.0277-0.0368-0.08460.00630.0243-0.0295-0.0127-0.0402-30.1594-28.9365-36.7474
80.0003-0.18220.62820.0361-0.38160.0000-0.0044-0.01880.04130.00540.0024-0.0182-0.03110.00800.00200.02310.0198-0.04330.00380.0077-0.0359-14.616159.8570-26.8129
91.29280.18691.84081.0546-1.19025.76210.0191-0.0395-0.02400.0683-0.0083-0.0397-0.20650.1134-0.01080.0311-0.1048-0.0848-0.15440.0057-0.1273-2.074049.2301-9.2927
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1{A|7:57}
2X-RAY DIFFRACTION2{B|7:169 233:268}
3X-RAY DIFFRACTION3{B|170:232}
4X-RAY DIFFRACTION4{B|269:342}
5X-RAY DIFFRACTION5{F|-1-39 127:171 255:281}
6X-RAY DIFFRACTION6{F|40:51 111:126 172:216 238:254}
7X-RAY DIFFRACTION7{F|52:110 217:237}
8X-RAY DIFFRACTION8{F|282:293}
9X-RAY DIFFRACTION9{F|294:391}

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