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- PDB-6tit: VSV G_440 -

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Basic information

Entry
Database: PDB / ID: 6tit
TitleVSV G_440
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / viral fusion protein / vsv / vesicular stomatitis virus / glycoprotein / ectodomain
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / symbiont entry into host cell / viral envelope / virion attachment to host cell / membrane / ACETATE ION / DI(HYDROXYETHYL)ETHER / Glycoprotein
Function and homology information
Biological speciesRecombinant vesicular stomatitis Indiana virus rVSV-G/GFP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsAlbertini, A.A. / Belot, L. / Abouhamdan, A. / Gaudin, Y.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0020 France
Foundation for Medical Research (France)DEQ20120323711 France
CitationJournal: Cell Rep / Year: 2020
Title: Identification of a pH-Sensitive Switch in VSV-G and a Crystal Structure of the G Pre-fusion State Highlight the VSV-G Structural Transition Pathway.
Authors: Beilstein, F. / Abou Hamdan, A. / Raux, H. / Belot, L. / Ouldali, M. / Albertini, A.A. / Gaudin, Y.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,76714
Polymers48,4091
Non-polymers1,35713
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-36 kcal/mol
Surface area21590 Å2
Unit cell
Length a, b, c (Å)120.950, 120.950, 200.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-806-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein Glycoprotein /


Mass: 48409.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: B7UCZ5
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 229 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.37 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG8000, 0.15M calcium acetate, 0.15M HEPES pH7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.07→44.82 Å / Num. obs: 52870 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.9 / Net I/σ(I): 8.27
Reflection shellResolution: 2.07→2.35 Å / Num. unique obs: 6568 / CC1/2: 0.396

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5i2s

5i2s


Resolution: 2.07→44.82 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.39
RfactorNum. reflection% reflection
Rfree0.2417 2600 4.92 %
Rwork0.2066 --
obs0.2083 52860 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 243.26 Å2 / Biso mean: 59.2694 Å2 / Biso min: 21.71 Å2
Refinement stepCycle: final / Resolution: 2.07→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 64 219 3689
Biso mean--67.9 48 -
Num. residues----432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.110.36211240.3422384250892
2.11-2.150.31021510.30225822733100
2.15-2.20.27031360.292325972733100
2.2-2.240.28551310.26926172748100
2.24-2.30.3431200.263326162736100
2.3-2.350.29911310.251926182749100
2.35-2.420.23221260.235526342760100
2.42-2.490.24791670.233525722739100
2.49-2.570.25691530.217726312784100
2.57-2.660.21791300.217926332763100
2.66-2.770.2781250.226226282753100
2.77-2.890.29611310.217426532784100
2.89-3.050.23761410.208426462787100
3.05-3.240.22021460.197826412787100
3.24-3.490.21661200.193326982818100
3.49-3.840.19871390.183126902829100
3.84-4.390.20781370.163527132850100
4.39-5.530.21411330.162227722905100
5.53-44.820.27481590.231929353094100

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