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Yorodumi- PDB-1rer: Crystal structure of the homotrimer of fusion glycoprotein E1 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rer | |||||||||
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Title | Crystal structure of the homotrimer of fusion glycoprotein E1 from Semliki Forest Virus. | |||||||||
Components | Structural polyprotein | |||||||||
Keywords | VIRAL PROTEIN / Envelope glycoprotein / Membrane fusion / virus. | |||||||||
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 / MAD, MIR / Resolution: 3.2 Å | |||||||||
Authors | Gibbons, D.L. / Vaney, M.C. / Roussel, A. / Vigouroux, A. / Reilly, B. / Kielian, M. / Rey, F.A. | |||||||||
Citation | Journal: Nature / Year: 2004 Title: Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus. Authors: Gibbons, D.L. / Vaney, M.C. / Roussel, A. / Vigouroux, A. / Reilly, B. / Lepault, J. / Kielian, M. / 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 Authors: LESCAR, J. / ROUSSEL, A. / WIEN, M.W. / NAVAZA, J. / FULLER, S.D. / WENGLER, G. / REY, F.A. #2: Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Visualization of the target-membrane-inserted fusion protein of Semliki Forest virus by combined electron microscopy and crystallography. Authors: Gibbons, D.L. / Erk, I. / Reilly, B. / Navaza, J. / Kielian, M. / Rey, F.A. / Lepault, J. #3: Journal: J.VIROL. / Year: 2002 Title: Molecular dissection of the Semliki Forest virus homotrimer reveals two functionally distinct regions of the fusion protein. Authors: Gibbons, D.L. / Lepault, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rer.cif.gz | 236.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rer.ent.gz | 196.5 KB | Display | PDB format |
PDBx/mmJSON format | 1rer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rer_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1rer_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1rer_validation.xml.gz | 53 KB | Display | |
Data in CIF | 1rer_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/1rer ftp://data.pdbj.org/pub/pdb/validation_reports/re/1rer | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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Details | The biological assembly is the homotrimer from the asymmetric unit. |
-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42690.125 Da / Num. of mol.: 3 / Fragment: Spike glycoprotein E1 / Source method: isolated from a natural source Details: Contains: Coat protein C (EC 3.4.21.-) (Capsid protein C); Spike glycoprotein E3; Spike glycoprotein E2; Spike glycoprotein E1 Source: (natural) Semliki forest virus / Genus: Alphavirus / References: UniProt: P03315 |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4) ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 147 molecules
#5: Chemical | #6: Chemical | ChemComp-HO / #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 15 |
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-Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.1 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG 400, NaBr, detergent DDAO, HO3+, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 3, 2003 / Details: Si(111) monochromator | ||||||||||||||||||||
Radiation | Monochromator: Sagitally focused Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→20 Å / Num. all: 43822 / Num. obs: 40912 |
-Processing
Software |
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Refinement | Method to determine structure: MAD, MIR / Resolution: 3.2→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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LS refinement shell | Resolution: 3.2→3.23 Å
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |