[English] 日本語
Yorodumi- PDB-1i9w: CRYSTAL STRUCTURE OF THE FUSION GLYCOPROTEIN E1 FROM SEMLIKI FORE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i9w | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE FUSION GLYCOPROTEIN E1 FROM SEMLIKI FOREST VIRUS | ||||||
Components | FUSION PROTEIN E1 | ||||||
Keywords | VIRAL PROTEIN / envelope glycoprotein / virus / 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 | Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Wengler, G. / Rey, F.A. | ||||||
Citation | 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. Authors: Lescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Wengler, G. / Rey, F.A. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). No matrices were provided to generate the icosohedral particle consisting of this protein from these coordinates. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i9w.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i9w.ent.gz | 12.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i9w_validation.pdf.gz | 355 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1i9w_full_validation.pdf.gz | 355 KB | Display | |
Data in XML | 1i9w_validation.xml.gz | 1.4 KB | Display | |
Data in CIF | 1i9w_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/1i9w ftp://data.pdbj.org/pub/pdb/validation_reports/i9/1i9w | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 42619.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Semliki forest virus / Genus: Alphavirus / References: UniProt: P03315 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8 / Details: PEG 8K, pH 8.0, VAPOR DIFFUSION, temperature 294K | ||||||||||||||||||||
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: ID14-3 / Wavelength: 0.945 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 22, 1998 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.945 Å / Relative weight: 1 |
Reflection | Resolution: 3→15 Å / Num. all: 13318 / Num. obs: 11519 / % possible obs: 86.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.5 |
Reflection shell | Highest resolution: 3 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3 |
Reflection | *PLUS Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS Rmerge(I) obs: 0.252 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 3→15 Å / Details: The coordinates contain only CA atoms.
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→15 Å
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Num. reflection obs: 10353 / Rfactor obs: 0.275 / Rfactor Rfree: 0.337 / Rfactor Rwork: 0.275 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |