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- PDB-7p5b: Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (s... -

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Basic information

Entry
Database: PDB / ID: 7p5b
TitleVariant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (serine 319 to alanine), single O-linked glycosylated at Ser317
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: 1.13 Å
AuthorsGkeka, A. / Aresta-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 2.2Oct 16, 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)54,9393
Polymers53,6861
Non-polymers1,2532
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint26 kcal/mol
Surface area16400 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)164,8189
Polymers161,0583
Non-polymers3,7596
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15500 Å2
ΔGint35 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.007, 129.007, 129.007
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-921-

HOH

21A-1025-

HOH

31A-1136-

HOH

41A-1142-

HOH

51A-1156-

HOH

61A-1165-

HOH

71A-1187-

HOH

81A-1188-

HOH

91A-1193-

HOH

101A-1196-

HOH

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Components

#1: Protein Variant surface glycoprotein


Mass: 53686.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Serine319 from the original 6ELC structure has been mutated to an Alanine.
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES153.14, Tb427.BES65.13 / Cell line (production host): VSG3S319A / 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.: 1 / 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.: 497 / 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: 25% PEG 3350, 300mM NaCl, 100mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.13→40.8 Å / Num. obs: 132433 / % possible obs: 96.6 % / Redundancy: 39 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.07786 / Rpim(I) all: 0.0125 / Rrim(I) all: 0.07886 / Net I/σ(I): 23.97
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 28.4 % / Rmerge(I) obs: 6.968 / Mean I/σ(I) obs: 0.42 / Num. unique obs: 8709 / CC1/2: 0.169 / CC star: 0.538 / Rpim(I) all: 1.324 / Rrim(I) all: 7.094 / % possible all: 66.13

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Processing

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

6elc


Resolution: 1.13→40.8 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 6420 5.02 %
Rwork0.1754 121519 -
obs0.1766 132433 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.41 Å2 / Biso mean: 25.6297 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 1.13→40.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2585 0 153 497 3235
Biso mean--32.57 32.75 -
Num. residues----358
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 (%)
1.13-1.140.3209620.34081049111125
1.14-1.160.32681530.33853045319874
1.16-1.170.37161960.34342044400100
1.17-1.190.32121760.327641964372100
1.19-1.20.32532340.320541804414100
1.2-1.220.3262450.324741424387100
1.22-1.230.30892410.305641074348100
1.23-1.250.33392210.292442064427100
1.25-1.270.32932090.269941494358100
1.27-1.290.27642340.266542084442100
1.29-1.320.25372200.255641434363100
1.32-1.340.26062400.238341324372100
1.34-1.370.26532090.239641884397100
1.37-1.390.25532310.220441494380100
1.39-1.420.23972040.223742474451100
1.42-1.460.23192390.21541514390100
1.46-1.490.23812090.213641744383100
1.49-1.530.26332190.206741994418100
1.53-1.580.22782430.190141294372100
1.58-1.630.20762310.18742114442100
1.63-1.690.21142200.183841744394100
1.69-1.760.21572080.179842164424100
1.76-1.840.20532360.178141754411100
1.84-1.930.20092080.178442054413100
1.93-2.050.18292330.157742014434100
2.05-2.210.17712040.155642324436100
2.21-2.430.18422290.153842254454100
2.43-2.790.18572310.153542284459100
2.79-3.510.18352120.155842744486100
3.51-40.80.15712230.15243804603100
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)
11.3861.75841.64162.16331.98521.99820.0751-0.0602-0.12230.0219-0.0093-0.16970.0137-0.1064-0.09990.14920.0079-0.00780.15690.00350.17918.818523.66796.1833
21.7122-0.5158-0.74993.4061-0.41282.1247-0.04460.11030.1635-0.3750.18060.15510.0534-0.2053-0.11830.1772-0.0388-0.01410.19680.03790.1353-4.4988.276-23.3004
32.76791.70531.79924.72472.53693.7798-0.1791-0.01150.2342-0.3154-0.06560.2508-0.1605-0.09110.25040.13880.0055-0.0250.13380.03080.1282-3.67925.317-11.1835
41.04941.01360.74562.47561.61722.67320.04260.0466-0.0117-0.0672-0.0224-0.0162-0.0217-0.0893-0.00290.120.01350.00730.11750.01480.143923.393543.25210.8212
50.53570.32140.02561.28-0.1190.76180.06830.01530.01650.1137-0.027-0.05170.0082-0.0397-0.0440.16130.0093-0.00880.13910.01410.160524.654140.025620.8007
60.89273.0572.30416.16665.38713.95050.1388-0.0343-0.03250.2785-0.0725-0.16690.2333-0.0488-0.04880.2207-0.0085-0.02010.1776-0.01760.20586.855110.9075-0.9661
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 167 )A136 - 167
4X-RAY DIFFRACTION4chain 'A' and (resid 168 through 242 )A168 - 242
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 340 )A243 - 340
6X-RAY DIFFRACTION6chain 'A' and (resid 341 through 386 )A341 - 386

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