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- PDB-1i9w: CRYSTAL STRUCTURE OF THE FUSION GLYCOPROTEIN E1 FROM SEMLIKI FORE... -

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Basic information

Entry
Database: PDB / ID: 1i9w
TitleCRYSTAL STRUCTURE OF THE FUSION GLYCOPROTEIN E1 FROM SEMLIKI FOREST VIRUS
ComponentsFUSION PROTEIN E1
KeywordsVIRAL 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesSemliki forest virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsLescar, J. / Roussel, A. / Wien, M.W. / Navaza, J. / Fuller, S.D. / Wengler, G. / Wengler, G. / Rey, F.A.
CitationJournal: 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
DepositionMar 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FUSION PROTEIN E1


Theoretical massNumber of molelcules
Total (without water)42,6191
Polymers42,6191
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.46, 79.46, 334.76
Angle α, β, γ (deg.)90, 90, 120
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein FUSION PROTEIN E1 / / SPIKE GLYCOPROTEIN E1 / Coordinate model: Cα atoms only


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
21-5 %(w/v)PEG800011
3pure paraffin oil12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.945 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 22, 1998
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 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 shellHighest 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

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 3→15 Å / Details: The coordinates contain only CA atoms.
RfactorNum. reflection% reflection
Rfree0.344 1166 -
Rwork0.275 --
all-13318 -
obs-11519 86.5 %
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms369 0 0 0 369
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

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