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- PDB-6z8h: Crystal structure of Variant Surface Glycoprotein VSG13 -

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Basic information

Entry
Database: PDB / ID: 6z8h
TitleCrystal structure of Variant Surface Glycoprotein VSG13
ComponentsVariant surface glycoprotein MITat 1.13
KeywordsMEMBRANE PROTEIN / Variant Surface Glycoprotein / Immune Recognition / Immune Evasion / Trypanosomiasis
Function / homologyTrypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / evasion of host immune response / plasma membrane / Variant surface glycoprotein MITat 1.13
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsStebbins, C.E. / Hempelmann, A. / Van Straaten, M. / Zeelen, J.
CitationJournal: Nat Microbiol / Year: 2021
Title: Structure of trypanosome coat protein VSGsur and function in suramin resistance.
Authors: Zeelen, J. / van Straaten, M. / Verdi, J. / Hempelmann, A. / Hashemi, H. / Perez, K. / Jeffrey, P.D. / Halg, S. / Wiedemar, N. / Maser, P. / Papavasiliou, F.N. / Stebbins, C.E.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variant surface glycoprotein MITat 1.13
B: Variant surface glycoprotein MITat 1.13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,2089
Polymers107,5432
Non-polymers1,6657
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-42 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.717, 68.341, 156.903
Angle α, β, γ (deg.)90.000, 92.548, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Variant surface glycoprotein MITat 1.13


Mass: 53771.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Glycosylated at N260 / Source: (natural) Trypanosoma brucei (eukaryote) / References: UniProt: Q58NS4
#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: 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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.8-2.0 M (NH4)2SO4, 100 mM Tris.Cl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.378→48.14 Å / Num. obs: 155980 / % possible obs: 97.09 % / Redundancy: 3 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rpim(I) all: 0.03368 / Net I/σ(I): 8.07
Reflection shellResolution: 1.378→1.428 Å / Num. unique obs: 15141 / CC1/2: 0.84 / % possible all: 94.49

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z8G

6z8g


Resolution: 1.38→48.14 Å / SU ML: 0.1897 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.7523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 1636 1.05 %
Rwork0.2176 154044 -
obs0.2178 155680 97.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.18 Å2
Refinement stepCycle: LAST / Resolution: 1.38→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5256 0 105 421 5782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01075435
X-RAY DIFFRACTIONf_angle_d1.12277364
X-RAY DIFFRACTIONf_chiral_restr0.0779887
X-RAY DIFFRACTIONf_plane_restr0.0092945
X-RAY DIFFRACTIONf_dihedral_angle_d14.49612052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.4431330.401712437X-RAY DIFFRACTION94.34
1.42-1.460.34831340.344712595X-RAY DIFFRACTION95.77
1.46-1.520.32131330.296712528X-RAY DIFFRACTION94.87
1.52-1.580.28981350.266812687X-RAY DIFFRACTION96.49
1.58-1.650.30741330.249612669X-RAY DIFFRACTION96.5
1.65-1.740.24341380.231812885X-RAY DIFFRACTION97.46
1.74-1.850.29431360.228212892X-RAY DIFFRACTION97.62
1.85-1.990.27521370.219212894X-RAY DIFFRACTION97.8
1.99-2.190.28411380.220213074X-RAY DIFFRACTION98.55
2.19-2.50.22151390.207313091X-RAY DIFFRACTION99.07
2.5-3.160.20051400.220513136X-RAY DIFFRACTION98.86
3.16-48.140.21361400.189113156X-RAY DIFFRACTION97.71

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