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- PDB-2ala: Crystal structure of the Semliki Forest Virus envelope protein E1... -

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Basic information

Entry
Database: PDB / ID: 2ala
TitleCrystal structure of the Semliki Forest Virus envelope protein E1 in its monomeric conformation.
ComponentsStructural polyprotein (P130)
KeywordsVIRAL 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
Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / 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 ...Tick-borne Encephalitis virus Glycoprotein, domain 1 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesSemliki forest virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsRoussel, 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
DepositionAug 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structural polyprotein (P130)


Theoretical massNumber of molelcules
Total (without water)42,6901
Polymers42,6901
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.380, 79.380, 335.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-430-

HOH

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Components

#1: Protein Structural polyprotein (P130)


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 / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 3.6 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
21-5 %(w/v)PEG800011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.945 Å
DetectorDetector: CCD / Date: Sep 29, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.31868 1232 10.4 %RANDOM
Rwork0.26654 ---
obs0.27199 10604 87.9 %-
all-13467 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.062 Å2
Baniso -1Baniso -2Baniso -3
1--3.51 Å2-1.76 Å20 Å2
2---3.51 Å20 Å2
3---5.27 Å2
Refinement stepCycle: LAST / Resolution: 3→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 0 88 3023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223020
X-RAY DIFFRACTIONr_bond_other_d0.0010.022610
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9474125
X-RAY DIFFRACTIONr_angle_other_deg0.70736121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65224.298121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36615466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6361510
X-RAY DIFFRACTIONr_chiral_restr0.060.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined0.1750.2697
X-RAY DIFFRACTIONr_nbd_other0.1580.22872
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21471
X-RAY DIFFRACTIONr_nbtor_other0.0780.21858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0580.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1010.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1841.52457
X-RAY DIFFRACTIONr_mcbond_other0.0171.5768
X-RAY DIFFRACTIONr_mcangle_it0.2123129
X-RAY DIFFRACTIONr_scbond_it0.24631310
X-RAY DIFFRACTIONr_scangle_it0.3784.5996
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.536 72 -
Rwork0.38 657 -
obs--76.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.93960.7149-4.03731.3447-2.679215.76420.62780.1654-0.41390.1736-0.460.0164-0.323-1.3362-0.16780.7646-0.1969-0.1680.15180.0940.1139-12.70851.653171.765
23.6044.90195.05788.6947-0.315719.6051-0.80840.15370.73790.28630.34451.9061-1.9592-2.36320.46380.91510.01820.01740.92710.04990.9273-38.09741.054217.214
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 289
2X-RAY DIFFRACTION2A290 - 384
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.318 / Rfactor Rwork: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.028
X-RAY DIFFRACTIONr_chiral_restr0.061
LS refinement shell
*PLUS
Rfactor Rfree: 0.537 / Rfactor Rwork: 0.38

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