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- PDB-1lg7: Crystal structure of Vesicular Stomatitis Virus Matrix Protein -

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Basic information

Entry
Database: PDB / ID: 1lg7
TitleCrystal structure of Vesicular Stomatitis Virus Matrix Protein
ComponentsVSV matrix protein
KeywordsVIRAL PROTEIN / VIRUS MATRIX
Function / homology
Function and homology information


host cell nuclear membrane / viral budding via host ESCRT complex / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host gene expression / structural constituent of virion / viral envelope / virion membrane
Similarity search - Function
VSV matrix protein / VSV matrix protein / Vesiculovirus matrix / VSV matrix superfamily / Vesiculovirus matrix protein / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesVesicular stomatitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.96 Å
AuthorsGaudier, M. / Gaudin, Y. / Knossow, M.
Citation
Journal: EMBO J. / Year: 2002
Title: Crystal structure of vesicular stomatitis virus matrix protein.
Authors: Gaudier, M. / Gaudin, Y. / Knossow, M.
#1: Journal: Virology / Year: 2001
Title: Cleavage of Vesicular Stomatitis Virus Matrix Protein Prevents Self-association and Leads to Crystallization
Authors: Gaudier, M. / Gaudin, Y. / Knossow, M.
History
DepositionApr 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 999 SEQUENCE Author informed that protein sequence under study has not yet been deposited in any ... SEQUENCE Author informed that protein sequence under study has not yet been deposited in any sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VSV matrix protein


Theoretical massNumber of molelcules
Total (without water)21,0111
Polymers21,0111
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: VSV matrix protein

A: VSV matrix protein

A: VSV matrix protein

A: VSV matrix protein


Theoretical massNumber of molelcules
Total (without water)84,0444
Polymers84,0444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area6440 Å2
ΔGint-42 kcal/mol
Surface area28590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.690, 80.690, 51.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein VSV matrix protein


Mass: 21011.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vesicular stomatitis virus / Genus: Vesiculovirus / Strain: Indiana - Orsay / References: UniProt: Q8B0H2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 2000 monometylether, sodium chloride, sodium acetate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: Gaudier, M., (2001) Virology, 288, 308.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.5
2100 mM1dropNaCl
35 mg/mlprotein1drop
424 %PEG2000 MME1reservoir
50.2 Msodium acetate1reservoir
60.1 M1reservoirNaCl
70.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 17, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→25 Å / Num. all: 210584 / Num. obs: 209741 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 / Net I/σ(I): 30
Reflection shellResolution: 1.96→2.01 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.41 / % possible all: 95.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 12771 / Num. measured all: 209741 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 95.3 % / Rmerge(I) obs: 0.41

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.96→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 620 -Random
Rwork0.208 ---
all0.218 12771 --
obs0.218 12680 99.3 %-
Solvent computationBsol: 44.7872 Å2 / ksol: 0.335821 e/Å3
Displacement parametersBiso mean: 29.7033 Å2
Refinement stepCycle: LAST / Resolution: 1.96→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 0 115 1451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d1.516
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.028
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d2.455
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d3.055
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 1.96→2.03 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.322 --
Rwork0.2375 1107 -
obs--93.8 %
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 12032 / Rfactor all: 0.218 / Rfactor obs: 0.206 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_deg1.47
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg2.455
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg3.055
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / Rfactor Rwork: 0.239 / Rfactor obs: 0.239

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