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- PDB-7p59: Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) with two ... -

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Basic information

Entry
Database: PDB / ID: 7p59
TitleVariant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) with two O-linked post-translational modifications
ComponentsVariant surface glycoprotein
KeywordsMEMBRANE PROTEIN / Variant Surface Glycoprotein / Coat / Trypanosoma brucei / O-glycosylation / O-glycans / Immune Evasion / African trypanosome / antigenic variation / post-translational modification / VSG / parasite / sleeping sickness
Function / homologyTrypanosome variant surface glycoprotein, B-type, N-terminal domain / Trypanosomal VSG domain / Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / side of membrane / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsGkeka, A. / Arest-Branco, F. / Stebbins, C.E. / Papavasiliou, F.N.
Citation
Journal: Cell Rep / Year: 2023
Title: Immunodominant surface epitopes power immune evasion in the African trypanosome.
Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / van Straaten, M. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Verdi, J.P. / Stebbins, ...Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / van Straaten, M. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Verdi, J.P. / Stebbins, C.E. / Papavasiliou, F.N.
#1: Journal: Biorxiv / Year: 2022
Title: Immunodominant surface epitopes power immune evasion in the African trypanosome
Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Stebbins, C.E. / Papavasiliou, F.N.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0Apr 5, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_gen / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3684
Polymers53,9341
Non-polymers1,4333
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The N-terminal domain is a monomer by gel filtration chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint30 kcal/mol
Surface area16600 Å2
MethodPISA
2
A: Variant surface glycoprotein
hetero molecules

A: Variant surface glycoprotein
hetero molecules

A: Variant surface glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,10312
Polymers161,8033
Non-polymers4,3009
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area16550 Å2
ΔGint43 kcal/mol
Surface area40630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.155, 129.155, 129.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-861-

HOH

21A-931-

HOH

31A-979-

HOH

41A-980-

HOH

51A-993-

HOH

61A-995-

HOH

71A-996-

HOH

81A-997-

HOH

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Components

#1: Protein Variant surface glycoprotein / VSG3 MITat1.3 VSG224


Mass: 53934.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VSG3 is O-linked glycosylated on Ser317 and Ser319 with Glucose.
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES153.14, Tb427.BES65.13 / Cell line (production host): 224KI (VSG3WT) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: B3GVK1
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 295 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 250mM NaCl, 100mM Tris, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→45.66 Å / Num. obs: 93285 / % possible obs: 99.94 % / Redundancy: 19.9 % / Biso Wilson estimate: 17.02 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08937 / Rpim(I) all: 0.02045 / Rrim(I) all: 0.0917 / Net I/σ(I): 21.27
Reflection shellResolution: 1.27→1.318 Å / Redundancy: 19.1 % / Rmerge(I) obs: 2.497 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 9281 / CC1/2: 0.513 / CC star: 0.823 / Rpim(I) all: 0.5849 / Rrim(I) all: 2.565 / % possible all: 99.66

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ELC

6elc


Resolution: 1.27→45.66 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 9132 5.01 %
Rwork0.1747 173243 -
obs0.1758 93285 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.67 Å2 / Biso mean: 24.2062 Å2 / Biso min: 13.01 Å2
Refinement stepCycle: final / Resolution: 1.27→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 175 297 3072
Biso mean--26.65 28.76 -
Num. residues----360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.27-1.290.3093080.31385772608099
1.29-1.30.42153040.394357686072100
1.3-1.320.32353050.320658066111100
1.32-1.330.26573050.286257626067100
1.33-1.350.31373030.277957756078100
1.35-1.370.28783020.282856915993100
1.37-1.390.27913070.270358296136100
1.39-1.410.27593020.256557356037100
1.41-1.430.28373090.251358096118100
1.43-1.460.28063000.241258156115100
1.46-1.480.27413050.229757346039100
1.48-1.510.22913070.20658476154100
1.51-1.540.22473010.212957386039100
1.54-1.570.20383050.189257786083100
1.57-1.60.22712970.181457566053100
1.6-1.640.20453050.175957896094100
1.64-1.680.21353000.168757786078100
1.68-1.730.19273070.172258066113100
1.73-1.780.17843050.171257256030100
1.78-1.840.21113080.172957856093100
1.84-1.90.20993070.178258166123100
1.9-1.980.21083020.174156865988100
1.98-2.070.17063050.154858126117100
2.07-2.180.16263040.154257786082100
2.18-2.310.18963010.162257476048100
2.31-2.490.20943070.15658246131100
2.49-2.740.18373030.158557326035100
2.74-3.140.16963060.16258076113100
3.14-3.950.17413060.154257526058100
3.96-45.660.17313060.163857916097100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17092.06061.83232.1681.90871.5785-0.043-0.0639-0.0126-0.1465-0.0020.0053-0.0996-0.03910.06410.17390.0002-0.00390.15380.01190.1526.24998.692513.5829
22.06970.3611-1.35213.4213-1.24392.7404-0.1324-0.18870.0120.09640.1129-0.34180.17390.16440.06190.11710.0398-0.01190.1811-0.02210.176855.723.914936.8726
31.72313.25512.10365.77223.91972.61490.15370.0134-0.14070.24780.0328-0.31010.1770.0251-0.20480.16170.0098-0.04050.14920.0010.194539.069418.403628.9015
42.71441.09590.59422.36060.66921.3922-0.0299-0.0613-0.10320.0216-0.0234-0.05580.04670.02820.050.13650.01830.01370.10020.01170.116718.5788-14.8416.9011
50.7725-0.10320.02880.95240.27940.5518-0.0466-0.04960.0122-0.0174-0.02890.10650.0250.02570.07830.1590.0117-0.00470.14580.00780.166811.4943-7.73787.703
64.25216.0182.36877.76323.4811.11030.0283-0.06030.20070.004-0.11690.19960.0122-0.03640.15320.1836-0.0161-0.020.1528-0.00250.198433.21921.753225.8318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 69 )A20 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 135 )A70 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 184 )A136 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 242 )A185 - 242
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 340 )A243 - 340
6X-RAY DIFFRACTION6chain 'A' and (resid 341 through 387 )A341 - 387

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