[English] 日本語
Yorodumi- PDB-2ala: Crystal structure of the Semliki Forest Virus envelope protein E1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ala | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Semliki Forest Virus envelope protein E1 in its monomeric conformation. | ||||||
Components | Structural polyprotein (P130) | ||||||
Keywords | VIRAL PROTEIN / Envelope glycoprotein / Membrane Fusion | ||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / 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 | Semliki forest virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å | ||||||
Authors | Roussel, A. / Lescar, J. / Vaney, M.C. / Wengler, G. / Wengler, G. / Rey, F.A. | ||||||
Citation | 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. / Wengler, G. / Rey, F.A. #1: 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. #2: Journal: Nature / Year: 2004 Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ala.cif.gz | 80 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ala.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ala.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ala_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ala_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 2ala_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2ala_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/2ala ftp://data.pdbj.org/pub/pdb/validation_reports/al/2ala | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42690.125 Da / Num. of mol.: 1 / Fragment: Spike glycoprotein E1 / Source method: isolated from a natural source / Source: (natural) Semliki forest virus / Genus: Alphavirus / References: UniProt: P03315 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 63 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / pH: 8.1 / Details: PEG 8K, pH 8.1, EVAPORATION, temperature 293K | |||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Wengler, G., (1999) Virology, 257, 472. | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.945 Å |
Detector | Detector: CCD / Date: Sep 29, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.945 Å / Relative weight: 1 |
Reflection | Resolution: 3→39 Å / Num. all: 10666 / Num. obs: 10666 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3→3.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 5.4 / % possible all: 76.1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 39 Å / Num. measured all: 82854 |
Reflection shell | *PLUS Highest resolution: 3 Å / % possible obs: 76.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 3→39 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.809 / SU B: 52.882 / SU ML: 0.494 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 8 OF THE SOLVENT MOLECULES ADDED TO POSITIVE FOURIER DIFFERENCE PEAKS (ABOVE 3 SIGMA) ARE FURTHER THAN 3.5 ANGSTROMS AWAY FROM MACROMOLECULE. THE E1 PROTEIN IS GLYCOSYLATED at ASN 141. THE ...Details: 8 OF THE SOLVENT MOLECULES ADDED TO POSITIVE FOURIER DIFFERENCE PEAKS (ABOVE 3 SIGMA) ARE FURTHER THAN 3.5 ANGSTROMS AWAY FROM MACROMOLECULE. THE E1 PROTEIN IS GLYCOSYLATED at ASN 141. THE DENSITY WAS NOT CLEAR ENOUGH TO BUILD A SUGAR AT THIS LOCATION THUS WATER MOLECULES 71 AND 81 WERE PLACED INTO POSITIVE DENSITY NEAR THIS RESIDUE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.062 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.318 / Rfactor Rwork: 0.266 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.537 / Rfactor Rwork: 0.38 |