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Yorodumi- PDB-5khc: Structure of rubella virus E1 glycoprotein ectodomain fitted into... -
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-Basic information
Entry | Database: PDB / ID: 5khc | ||||||
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Title | Structure of rubella virus E1 glycoprotein ectodomain fitted into sub-tomogram averaged surface spike density of rubella virus | ||||||
Components | E1 glycoprotein | ||||||
Keywords | VIRAL PROTEIN / Rubella virus / surface glycoprotein spike / E1-E2 heterodimer | ||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding ...T=4 icosahedral viral capsid / host cell Golgi membrane / host cell mitochondrion / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / RNA binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Rubella virus | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 11.1 Å | ||||||
Authors | Mangala Prasad, V. / Klose, T. / Rossmann, M.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: PLoS Pathog / Year: 2017 Title: Assembly, maturation and three-dimensional helical structure of the teratogenic rubella virus. Authors: Vidya Mangala Prasad / Thomas Klose / Michael G Rossmann / Abstract: Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe ...Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus. Tomographic analyses of in vitro assembled nucleocapsids and virions provide a template for viral assembly. Comparisons of immature and mature virions show large rearrangements in the glycoproteins that may be essential for forming the infectious virions. These results present the first known example of a helical membrane-enveloped virus, while also providing a structural basis for its assembly and maturation pathway. | ||||||
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 | 5khc.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5khc.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 5khc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5khc_validation.pdf.gz | 614.4 KB | Display | wwPDB validaton report |
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Full document | 5khc_full_validation.pdf.gz | 614.6 KB | Display | |
Data in XML | 5khc_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 5khc_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/5khc ftp://data.pdbj.org/pub/pdb/validation_reports/kh/5khc | HTTPS FTP |
-Related structure data
Related structure data | 8248MC 8249C 8250C 8251C 5kheC 5khfC 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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-Components
#1: Protein | Mass: 50573.352 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 583-1018) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rubella virus / Production host: Cercopithecus aethiops (grivet) / References: UniProt: P08563 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Rubella virus E1-E2 glycoprotein spike / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.085 MDa / Experimental value: NO | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Rubella virus was purified from Vero cells. Glycoprotein spike volumes were extracted from the surface of virus tomograms. | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 11000 X / Nominal defocus max: 500 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 11.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7290 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
EM volume selection | Method: manual picking / Num. of tomograms: 15 / Num. of volumes extracted: 7500 | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: sumf | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4ADG Pdb chain-ID: A / Pdb chain residue range: 1-421 |