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- PDB-7p57: VSG2 mutant structure lacking the calcium binding pocket -

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Basic information

Entry
Database: PDB / ID: 7p57
TitleVSG2 mutant structure lacking the calcium binding pocket
ComponentsVariant surface glycoprotein MITAT 1.2
KeywordsMEMBRANE PROTEIN / Variant Surface Glycoprotein / Coat / Trypanosoma brucei / African trypanosome / Immune Evasion / antigenic variation / calcium binding / calcium
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / evasion of host immune response / side of membrane / plasma membrane / Variant surface glycoprotein MITAT 1.2
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.961 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 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Variant surface glycoprotein MITAT 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7202
Polymers50,9711
Non-polymers7491
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, The biological assembly is a dimer., isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint20 kcal/mol
Surface area17980 Å2
MethodPISA
2
A: Variant surface glycoprotein MITAT 1.2
hetero molecules

A: Variant surface glycoprotein MITAT 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4404
Polymers101,9432
Non-polymers1,4972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area11480 Å2
ΔGint-7 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.015, 96.015, 108.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

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Components

#1: Protein Variant surface glycoprotein MITAT 1.2 / VSG 221


Mass: 50971.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: VSG2 "AAA mutant" (D208, N209, and D210 each mutated to alanine).
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Cell line (production host): FAB 3.6.4 (VSG2-AAA) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 39% PEG400

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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: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.961→48.01 Å / Num. obs: 36675 / % possible obs: 99.24 % / Redundancy: 19.7 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09816 / Rpim(I) all: 0.02123 / Rrim(I) all: 0.1006 / Net I/σ(I): 20.27
Reflection shellResolution: 1.961→2.031 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.8934 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 3341 / CC1/2: 0.557 / CC star: 0.846 / Rpim(I) all: 0.4747 / Rrim(I) all: 1.023 / % possible all: 92.39

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSG

1vsg


Resolution: 1.961→48.01 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 3400 5 %
Rwork0.1603 64591 -
obs0.162 36675 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.86 Å2 / Biso mean: 43.8988 Å2 / Biso min: 21.36 Å2
Refinement stepCycle: final / Resolution: 1.961→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 50 239 2953
Biso mean--58.31 46.03 -
Num. residues----359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.961-1.98910.3479940.3575179866
1.9891-2.01880.35631300.313245590
2.0188-2.05030.28791390.2778267697
2.0503-2.08390.29461440.2655275399
2.0839-2.11980.28021490.22322735100
2.1198-2.15840.24411420.20352720100
2.1584-2.19990.21591450.18072741100
2.1999-2.24480.18831420.16672768100
2.2448-2.29360.20321460.17022748100
2.2936-2.3470.17611440.15662753100
2.347-2.40570.21511490.14562754100
2.4057-2.47070.1681450.15282709100
2.4707-2.54340.18461450.15022733100
2.5434-2.62550.18221460.14582771100
2.6255-2.71930.20221440.14372747100
2.7193-2.82820.17031450.15372770100
2.8282-2.95690.23871410.16612726100
2.9569-3.11280.21151410.17572757100
3.1128-3.30770.25151470.17952745100
3.3077-3.56310.19031470.16742728100
3.5631-3.92150.16831470.14492746100
3.9215-4.48860.16131390.12292756100
4.4886-5.65370.14721450.14042763100
5.6537-48.010.17231440.14332739100
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)
12.9789-3.2781-0.51066.85851.19160.74730.15650.3118-0.3089-0.1233-0.0977-0.25970.13320.081-0.0610.2981-0.0169-0.05370.3131-0.0780.299-2.3456-10.686420.1191
27.4673-5.31722.27214.7829-1.91981.412-0.0899-0.2151-0.26210.09760.18460.3291-0.0348-0.243-0.10730.2436-0.0370.00260.23910.01650.2066-30.802120.999724.919
32.5478-1.2387-0.66233.01940.98311.53570.11860.3325-0.3379-0.16290.037-0.36620.18470.1304-0.13930.30130.0023-0.04970.3133-0.09620.33294.9795-11.564419.1615
43.23180.41453.26928.8586-3.33085.85950.05710.30720.0833-0.3588-0.08580.464-0.2002-0.1802-0.09870.31740.0126-0.02680.3173-0.04430.3371-11.7525-6.187218.9748
52.9947-1.21330.37862.1250.18281.09350.13010.1634-1.02320.2440.0931-0.36840.4340.1986-0.20970.50410.0625-0.15430.2914-0.0440.63538.4195-25.168828.9931
66.66261.99624.50192.2531.95183.25490.3007-1.139-0.21140.9749-0.1680.05970.2743-0.3642-0.13560.4422-0.0464-0.01950.36570.00970.2843-5.7779-12.838535.6786
71.97821.73620.09692.00790.39950.1867-0.0294-0.1305-0.0961-0.27390.18930.6616-0.0664-0.0375-0.16780.2761-0.0221-0.01390.32850.00290.3252-18.77560.488628.5411
88.0523-3.6975-4.1987.98663.04464.6016-0.4733-0.9189-0.73270.98150.40660.73980.44620.22570.1840.33390.02010.0130.43910.18990.4396-39.827216.469134.207
95.35891.7704-1.56524.5449-1.72534.7744-0.07920.1895-0.2762-0.22690.18630.43870.2504-0.4642-0.09960.2390.0387-0.06580.24880.02790.3148-37.068922.836218.7155
103.7407-2.1481-5.40617.6686.69119.76750.54140.08530.4184-0.4613-0.3220.3977-1.2497-0.4267-0.36080.51960.05650.02570.37810.07490.3981-34.673741.591223.6614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:62)A27 - 62
2X-RAY DIFFRACTION2(chain A and resid 63:111)A63 - 111
3X-RAY DIFFRACTION3(chain A and resid 112:178)A112 - 178
4X-RAY DIFFRACTION4(chain A and resid 179:190)A179 - 190
5X-RAY DIFFRACTION5(chain A and resid 191:256)A191 - 256
6X-RAY DIFFRACTION6(chain A and resid 257:273)A257 - 273
7X-RAY DIFFRACTION7(chain A and resid 274:287)A274 - 287
8X-RAY DIFFRACTION8(chain A and resid 288:313)A288 - 313
9X-RAY DIFFRACTION9(chain A and resid 314:375)A314 - 375
10X-RAY DIFFRACTION10(chain A and resid 376:385)A376 - 385

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