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Yorodumi- PDB-2v33: High resolution crystal structure of domain III of E1 fusion glyc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v33 | ||||||
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Title | High resolution crystal structure of domain III of E1 fusion glycoprotein of Semliki Forest Virus | ||||||
Components | E1 ENVELOPE GLYCOPROTEIN | ||||||
Keywords | VIRAL PROTEIN / GLYCOPROTEIN / TRANSMEMBRANE | ||||||
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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | SEMLIKI FOREST VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Vaney, M.C. / Rey, F.A. | ||||||
Citation | Journal: To be Published Title: High Resolution Structure of Domain III from Class II Fusion Protein of Semliki Forest Virus Authors: Vaney, M.C. / Vigouroux, A. / Rey, F.A. #1: 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. / Rey, F.A. #2: 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. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v33.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v33.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/2v33 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/2v33 | HTTPS FTP |
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-Related structure data
Related structure data | 1rerS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.02945, 0.9988, 0.03936), Vector: |
-Components
#1: Protein | Mass: 9347.467 Da / Num. of mol.: 2 Fragment: DOMAIN III OF SPIKE GLYCOPROTEIN E1, RESIDUES 1107-1197 Source method: isolated from a natural source / Source: (natural) SEMLIKI FOREST VIRUS / References: UniProt: P03315 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 8K, 0.2M NA ACETATE, 0.1M CACO PH 6.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 4, 2005 |
Radiation | Monochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→28.57 Å / Num. obs: 31583 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.56 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RER (DOMAIN III) Resolution: 1.55→28.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.078 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ADOPT AN ALTERNATE CONFORMATION. FOR CHAIN A, THR 300A, THR 319A, VAL 336A, SER 362A, THR 307A, THR343A, LYS 351A, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ADOPT AN ALTERNATE CONFORMATION. FOR CHAIN A, THR 300A, THR 319A, VAL 336A, SER 362A, THR 307A, THR343A, LYS 351A, SER 357A. FOR CHAIN B, THR 300B, ,THR 302B,THR 305B,CYS 306B,THR 307B,LOOP PHE312B- GLY313B- -GLY314B, THR 319B,LOOP SER332B-HIS333B-SER334B-ASN 335B, ,VAL 336B,THR 338B,THR 343B,SER 357B,SER 362B,SER 371B. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→28.57 Å
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Refine LS restraints |
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