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Yorodumi- PDB-3muw: Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus -
+Open data
-Basic information
Entry | Database: PDB / ID: 3muw | ||||||
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Title | Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus | ||||||
Components | (Structural polyprotein) x 2 | ||||||
Keywords | VIRUS / icosahedral protein shell / icosahedral virus | ||||||
Function / homology | Function and homology information icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | Sindbis virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | Li, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Structural changes of envelope proteins during alphavirus fusion. Authors: Long Li / Joyce Jose / Ye Xiang / Richard J Kuhn / Michael G Rossmann / Abstract: Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope ...Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope glycoproteins, E1 and E2. The E2-E1 heterodimers form 80 trimeric spikes on the icosahedral virus surface, 60 with quasi-three-fold symmetry and 20 coincident with the icosahedral three-fold axes arranged with T = 4 quasi-symmetry. The E1 glycoprotein has a hydrophobic fusion loop at one end and is responsible for membrane fusion. The E2 protein is responsible for receptor binding and protects the fusion loop at neutral pH. The lower pH in the endosome induces the virions to undergo an irreversible conformational change in which E2 and E1 dissociate and E1 forms homotrimers, triggering fusion of the viral membrane with the endosomal membrane and then releasing the viral genome into the cytoplasm. Here we report the structure of an alphavirus spike, crystallized at low pH, representing an intermediate in the fusion process and clarifying the maturation process. The trimer of E2-E1 in the crystal structure is similar to the spikes in the neutral pH virus except that the E2 middle region is disordered, exposing the fusion loop. The amino- and carboxy-terminal domains of E2 each form immunoglobulin-like folds, consistent with the receptor attachment properties of E2. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3muw.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3muw.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 3muw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3muw_validation.pdf.gz | 960 KB | Display | wwPDB validaton report |
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Full document | 3muw_full_validation.pdf.gz | 959.5 KB | Display | |
Data in XML | 3muw_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 3muw_validation.cif.gz | 52.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/3muw ftp://data.pdbj.org/pub/pdb/validation_reports/mu/3muw | HTTPS FTP |
-Related structure data
Related structure data | 1121M 3muuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 41311.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Strain: Toto64 References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein | Mass: 38508.645 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Strain: Toto64 References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Details of virus | Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION | ||||||||||||
Natural host | Organism: Homo sapiens | ||||||||||||
Buffer solution | Name: TNE buffer / pH: 7.5 / Details: TNE buffer | ||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Details: This grid plus sample was kept at 100 K | ||||||||||||
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200T / Date: Jun 21, 2000 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 39220 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm |
Specimen holder | Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: CTF correction of each particle. | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: model-based common lines / Resolution: 9 Å / Num. of particles: 7085 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: sumf / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | PDB-ID: 3MUU Accession code: 3MUU / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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