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- PDB-3n42: Crystal structures of the mature envelope glycoprotein complex (f... -

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Entry
Database: PDB / ID: 3n42
TitleCrystal structures of the mature envelope glycoprotein complex (furin 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 / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily ...Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus core protein / 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 / Structural polyprotein
Function and homology information
Specimen sourceChikungunya virus / Chikungunya / virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3 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
Abstract: Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is ...Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is mediated by two viral glycoproteins, E1 and E2, which carry the main antigenic determinants and form an icosahedral shell at the virion surface. Glycoprotein E2, derived from furin cleavage of the p62 precursor into E3 and E2, is responsible for receptor binding, and E1 for membrane fusion. In the context of a concerted multidisciplinary effort to understand the biology of CHIKV, here we report the crystal structures of the precursor p62-E1 heterodimer and of the mature E3-E2-E1 glycoprotein complexes. The resulting atomic models allow the synthesis of a wealth of genetic, biochemical, immunological and electron microscopy data accumulated over the years on alphaviruses in general. This combination yields a detailed picture of the functional architecture of the 25 MDa alphavirus surface glycoprotein shell. Together with the accompanying report on the structure of the Sindbis virus E2-E1 heterodimer at acidic pH (ref. 3), this work also provides new insight into the acid-triggered conformational change on the virus particle and its inbuilt inhibition mechanism in the immature complex.
#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:
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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)99,0916
Polyers98,4283
Non-polymers6643
Water1,58588
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7690
ΔGint (kcal/M)-21
Surface area (Å2)37660
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)58.391, 90.678, 178.410
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 266-319 / Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster / References: UniProt:Q1H8W5
#2: Protein/peptide E2 envelope glycoprotein


Mass: 40600.785 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 330-667 / Source: (gene. exp.) Chikungunya virus / Strain: 05-115 / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster / References: UniProt:Q1H8W5
#3: Protein/peptide E1 envelope glycoprotein


Mass: 50356.223 Da / Num. of mol.: 1 / Fragment: polyprotein fragment residues 810-1202 / Source: (gene. exp.) Chikungunya virus / Strain: pMRBiP/V5 HisA / Plasmid name: pMRBiP/V5 HisA / Cell line (production host): SCHNEIDER 2 / Production host: Drosophila Melanogaster / References: UniProt:Q1H8W5

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Non-polymers , 3 types, 91 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.4 / Density percent sol: 48.74
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: Nov 13, 2009
RadiationMonochromator: S 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: 68.11 Å2 / D resolution high: 3 Å / D resolution low: 49.7 Å / Number obs: 18964 / Observed criterion sigma I: 0 / Rsym value: 0.123 / NetI over sigmaI: 9.2 / Redundancy: 3.7 / Percent possible obs: 96.4
Reflection shellHighest resolution: 3 Å / Lowest resolution: 3.16 Å / MeanI over sigI obs: 2 / Rsym value: 0.469 / Redundancy: 2.4 / Percent possible all: 82.2

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Processing

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

Correlation coeff Fo to Fc: 0.85 / Correlation coeff Fo to Fc free: 0.832 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Displacement parametersB iso mean: 59.22 Å2 / Aniso B11: -0.5004 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 13.0951 Å2 / Aniso B23: 0 Å2 / Aniso B33: -12.5948 Å2
Least-squares processR factor R free: 0.278 / R factor R work: 0.247 / R factor obs: 0.249 / Highest resolution: 3 Å / Lowest resolution: 44.6 Å / Number reflection R free: 980 / Number reflection obs: 18926 / Percent reflection R free: 5.18 / Percent reflection obs: 96.2
Refine analyzeLuzzati coordinate error obs: 0.55 Å
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 44.6 Å
Number of atoms included #LASTProtein: 6075 / Nucleic acid: 0 / Ligand: 42 / Solvent: 88 / Total: 6205
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076310HARMONIC2.000
X-RAY DIFFRACTIONt_angle_deg0.978613HARMONIC2.000
X-RAY DIFFRACTIONt_dihedral_angle_d2080SINUSOIDAL2.000
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes147HARMONIC2.000
X-RAY DIFFRACTIONt_gen_planes918HARMONIC5.000
X-RAY DIFFRACTIONt_it6310HARMONIC20.000
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.800
X-RAY DIFFRACTIONt_other_torsion19.340
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion847SEMIHARMONIC5.000
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_contact6322SEMIHARMONIC4.000
Refine LS shellHighest resolution: 3 Å / R factor R free: 0.3655 / R factor R work: 0.3033 / R factor all: 0.3066 / Lowest resolution: 3.16 Å / Number reflection R free: 131 / Number reflection R work: 2172 / Number reflection all: 2303 / Total number of bins used: 10 / Percent reflection R free: 5.69 / Percent reflection obs: 96.15
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.2512-0.70560.14271.6013-0.27010.0000-0.00090.00980.0330-0.0057-0.00500.0402-0.0343-0.01990.0059-0.03950.0195-0.06320.0222-0.02130.1451-56.6176-12.9749-35.3159
22.44752.83890.69515.85401.47900.7329-0.0155-0.02440.01680.3762-0.06170.13070.0299-0.10150.07720.0705-0.02720.1492-0.1991-0.0639-0.0259-36.0388-15.8476-17.4125
34.72070.0425-1.03630.68780.40782.1543-0.00040.0315-0.0942-0.05140.0098-0.01860.12940.0091-0.0095-0.0193-0.11060.06470.02580.00710.0503-50.1963-45.5195-31.6189
43.9550-1.38932.89981.31932.23243.5027-0.0065-0.1200-0.00050.1034-0.0067-0.0478-0.01050.07040.01320.0037-0.0825-0.1399-0.0478-0.0366-0.0079-3.506713.0088-9.1447
51.19071.5837-0.07882.3282-0.48121.1425-0.0009-0.0174-0.0146-0.0443-0.01450.03220.05890.00420.0154-0.0349-0.0455-0.05730.00910.01930.0516-12.772136.0262-28.0040
62.39971.9330-0.81715.19032.27263.78290.00760.0344-0.0272-0.0537-0.0337-0.0719-0.0544-0.00970.0261-0.10140.0078-0.0941-0.04920.02370.0708-18.18911.3197-33.6945
71.9558-0.52151.46653.50351.83860.87610.0056-0.0397-0.0598-0.0297-0.00790.05360.0558-0.00900.0024-0.02670.01270.01130.0323-0.0279-0.0297-30.2185-29.0831-36.5390
80.0000-0.10130.18720.00000.03110.0000-0.0018-0.01440.01450.0115-0.00480.0011-0.01370.00180.0066-0.00330.0072-0.01010.0150-0.0205-0.0136-14.551459.9645-26.5908
91.54102.04362.34100.9723-0.86837.7003-0.0032-0.01510.01870.0320-0.0162-0.0010-0.12500.04050.01940.0986-0.0791-0.1466-0.0740-0.0282-0.1196-1.937748.9606-9.1154
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1{A|7:58}
2X-RAY DIFFRACTION2{B|5:169 233:268}
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|294:393}

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