+Open data
-Basic information
Entry | Database: PDB / ID: 2yew | ||||||
---|---|---|---|---|---|---|---|
Title | Modeling Barmah Forest virus structural proteins | ||||||
Components |
| ||||||
Keywords | VIRUS / ALPHAVIRUS / MOLECULAR DYNAMICS | ||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity ...togavirin / T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding Similarity search - Function | ||||||
Biological species | BARMAH FOREST VIRUS | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å | ||||||
Authors | Kostyuchenko, V.A. / Jakana, J. / Liu, X. / Haddow, A.D. / Aung, M. / Weaver, S.C. / Chiu, W. / Lok, S.M. | ||||||
Citation | Journal: J Virol / Year: 2011 Title: The structure of barmah forest virus as revealed by cryo-electron microscopy at a 6-angstrom resolution has detailed transmembrane protein architecture and interactions. Authors: Victor A Kostyuchenko / Joanita Jakana / Xiangan Liu / Andrew D Haddow / Myint Aung / Scott C Weaver / Wah Chiu / Shee-Mei Lok / Abstract: Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, ...Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2yew.cif.gz | 691 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yew.ent.gz | 549.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yew_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2yew_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2yew_validation.xml.gz | 126.3 KB | Display | |
Data in CIF | 2yew_validation.cif.gz | 183.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/2yew ftp://data.pdbj.org/pub/pdb/validation_reports/ye/2yew | HTTPS FTP |
-Related structure data
Related structure data | 1886MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 28311.041 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BARMAH FOREST VIRUS / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P89946, togavirin #2: Protein | Mass: 46283.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BARMAH FOREST VIRUS / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P89946 #3: Protein | Mass: 46185.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BARMAH FOREST VIRUS / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P89946 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: BARMAH FOREST VIRUS / Type: VIRUS |
---|---|
Buffer solution | pH: 7.4 / Details: 0.05M Tris-HCl, pH 7.4, 0.1M NaCl, 0.001M EDTA |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: JEOL 3200FSC / Date: Jan 10, 2010 |
---|---|
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 4.1 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GENERIC GATAN |
Image scans | Num. digital images: 760 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: INDIVIDUAL PARTICLES | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: CROSS-COMMON LINES, MULTIPATH SIMULTANEOUS ANNEALING PROTOCOL Resolution: 5 Å / Num. of particles: 5169 / Nominal pixel size: 1.42 Å / Actual pixel size: 1.42 Å Details: THE MODELS WERE BUILD USING MODELLER FOR HOMOLOGY -BASED MODELLING AND USING VMD WITH NAMD FOR FLEXIBLE FITTING INTO CRYO-EM DENSITY. CHAIN A DOES NOT CONTAIN RNA-BINDING PART, ABOUT 80 N- ...Details: THE MODELS WERE BUILD USING MODELLER FOR HOMOLOGY -BASED MODELLING AND USING VMD WITH NAMD FOR FLEXIBLE FITTING INTO CRYO-EM DENSITY. CHAIN A DOES NOT CONTAIN RNA-BINDING PART, ABOUT 80 N-TERMINAL RESIDUES. THE STRUCTURE WAS MODELED BASED ON HOMOLOGY TO PROTEIN WITH KNOWN STURUCTURE AND CRYO-EM DENSITY FITTING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- 1886. (DEPOSITION ID: 7893). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
Atomic model building |
| ||||||||||||
Refinement | Highest resolution: 5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5 Å
|