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- PDB-2xfc: CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST... -
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Basic information
Entry | Database: PDB / ID: 2xfc | ||||||||||||||||||||||||
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Title | CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SEMLIKI FOREST VIRUS cryo-EM MAP | ||||||||||||||||||||||||
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![]() | VIRUS / RECEPTOR BINDING / MEMBRANE FUSION / ICOSAHEDRAL ENVELOPED VIRUS | ||||||||||||||||||||||||
Function/homology | Alphavirus E2 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Peptidase S3, togavirin / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E3 glycoprotein / Flavivirus glycoprotein, central and dimerisation domain superfamily ...Alphavirus E2 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Peptidase S3, togavirin / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E3 glycoprotein / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / host cell membrane / viral capsid / Immunoglobulin E-set / fusion of virus membrane with host endosome membrane / host cell cytoplasm / virion attachment to host cell / virion membrane / Peptidase S1, PA clan / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / identical protein binding / Structural polyprotein![]() | ||||||||||||||||||||||||
Specimen source | CHIKUNGUNYA VIRUS / ![]() ![]() | ||||||||||||||||||||||||
Method | Electron microscopy (9 Å resolution / Particle / Single particle) / Transmission electron microscopy | ||||||||||||||||||||||||
![]() | Voss, J.E. / Vaney, M.C. / Duquerroy, S. / Rey, F.A. | ||||||||||||||||||||||||
![]() | Journal: Mol. Cell / Year: 2000 Title: Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. ![]() Abstract: Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion ...Semliki Forest virus serves as a paradigm for membrane fusion and assembly. Our icosahedral reconstruction combined 5276 particle images from 48 cryo-electron micrographs and determined the virion structure to 9 A resolution. The improved resolution of this map reveals an N-terminal arm linking capsid subunits and defines the spike-capsid interaction sites. It illustrates the paired helical nature of the transmembrane segments and the elongated structures connecting them to the spike projecting domains. A 10 A diameter density in the fusion protein lines the cavity at the center of the spike. These clearly visible features combine with the variation in order between the layers to provide a framework for understanding the structural changes during the life cycle of an enveloped virus. | ||||||||||||||||||||||||
Validation Report | ![]() ![]() ![]() | ||||||||||||||||||||||||
Date | Deposition: May 21, 2010 / Release: Nov 24, 2010
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-Related structure data
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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Components
#1: Protein/peptide | Mass: 47460.934 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 810-1248 Source: (gene. exp.) CHIKUNGUNYA VIRUS / ![]() ![]() Strain: 05-115 / Plasmid name: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER / Strain (production host): SCHNEIDER 2 / References: UniProt:Q1H8W5 #2: Protein/peptide | Mass: 47374.086 Da / Num. of mol.: 4 / Fragment: ECTODOMAIN, RESIDUES 326-748 Source: (gene. exp.) CHIKUNGUNYA VIRUS / ![]() ![]() Strain: 05-115 / Plasmid name: PMRBIP/V5HISA / Production host: DROSOPHILA MELANOGASTER / Strain (production host): SCHNEIDER 2 / References: UniProt:Q1H8W5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE |
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Sample preparation
Component | Name: semliki forest virus / Type: VIRUS |
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Buffer solution | Details: Tris (10mM) NaCl (100 mM) ph 7.4 / pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Microscope model: FEI/PHILIPS CM200FEG/ST / Date: Jan 1, 1995 |
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Electron gun | Electron source: OTHER / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal magnification: 50000 / Nominal defocus max: 7628 nm / Nominal defocus min: 975 nm |
Image recording | Electron dose: 8 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation wavelength | Relative weight: 1 |
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Processing
Symmetry | Point symmetry: I |
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3D reconstruction | Resolution: 9 Å / Number of particles: 6000 Details: THE COMPLETE PARTICLE IS GENERATED BY BIOMT MATRICES. THE FIT WAS GENERATED WITH URO IN SINDBIS CRYO-EM MAP EMDB-1015 THAT WAS CORRECTED IN MAGNITUDE BY MULTIPLYING A FACTOR OF 1.038 AND USING PDB ENTRY 3N40 Symmetry type: POINT |
Least-squares process | Highest resolution: 9 Å |
Refine hist #LAST | Highest resolution: 9 Å |
Number of atoms included #LAST | Protein: 22420 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 22420 |