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- PDB-7p5a: Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (s... -

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Basic information

Entry
Database: PDB / ID: 7p5a
TitleVariant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (serine 317 to alanine), single O-linked glycosylated at Ser319
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 / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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

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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)55,1723
Polymers53,9181
Non-polymers1,2532
Water4,252236
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 area2110 Å2
ΔGint26 kcal/mol
Surface area16040 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)165,5159
Polymers161,7553
Non-polymers3,7596
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14680 Å2
ΔGint21 kcal/mol
Surface area39760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.396, 129.396, 129.396
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-911-

HOH

21A-921-

HOH

31A-931-

HOH

41A-935-

HOH

51A-936-

HOH

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Components

#1: Protein Variant surface glycoprotein


Mass: 53918.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Serine317 from the wild type VSG3 sequence has been mutated to alanine.
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES153.14, Tb427.BES65.13 / Cell line (production host): 224S317A (VSG3S317A) / 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.: 236 / Source method: isolated from a natural source / Formula: H2O
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

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: Aug 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→54.75 Å / Num. obs: 26355 / % possible obs: 99.89 % / Redundancy: 30.8 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1179 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.1198 / Net I/σ(I): 32.36
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8387 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2584 / CC1/2: 0.614 / CC star: 0.872 / Rpim(I) all: 0.3875 / Rrim(I) all: 0.9312 / % possible all: 99.12

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Processing

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

6elc


Resolution: 1.95→45.75 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / σ(F): 1.75 / Phase error: 22.3616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2132 1318 5 %
Rwork0.1816 25037 -
obs0.1832 26355 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.34 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 83 236 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422650
X-RAY DIFFRACTIONf_angle_d0.71333611
X-RAY DIFFRACTIONf_chiral_restr0.0383450
X-RAY DIFFRACTIONf_plane_restr0.0038462
X-RAY DIFFRACTIONf_dihedral_angle_d4.9501428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.030.32651430.31212714X-RAY DIFFRACTION97.54
2.03-2.120.2721440.20472745X-RAY DIFFRACTION99.97
2.12-2.230.22021470.18492788X-RAY DIFFRACTION100
2.23-2.370.24451450.17652764X-RAY DIFFRACTION100
2.37-2.550.23281460.17742760X-RAY DIFFRACTION99.93
2.55-2.810.22351460.18112782X-RAY DIFFRACTION100
2.81-3.220.22021460.19072784X-RAY DIFFRACTION100
3.22-4.050.18091480.16232806X-RAY DIFFRACTION100
4.06-45.750.18351530.16872894X-RAY DIFFRACTION99.97
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)
11.011510801241.184818823320.940331834781.439086088141.182835741751.0342002859-0.111761648157-0.0297773162129-0.0704731860327-0.2098079835190.0697427763289-0.0512547362758-0.156865485895-0.006451835957880.09223802639180.1883425034480.00686636487817-0.005829956028580.167825348448-0.00632431379720.17696655644426.1699149268.6089707176213.5470723681
20.948865276549-0.304003336607-0.2353518782271.317014196760.09006711494820.875146671438-0.0194276373596-0.146649729406-0.01926401253670.04829127461540.0529924879397-0.1786951141930.1368873928850.125428463467-0.03240264527010.2173196978640.025536149346-0.009561485099780.2421288575890.0007905420547840.2117155923851.018619108425.342500049436.4543030259
32.088745975611.359447285150.5421620666142.584223202451.124088356610.919067074167-0.000802643058638-0.0235382164517-0.06525753339920.0381959940196-0.0302236296475-0.08330422276730.004736273435410.009584744497290.02331128540430.1832512055420.0167881561371-0.005248218080990.1503076878180.02269790182090.16789869689621.6494352448-10.62022368719.1754209032
40.3370793128840.232710020930.1749823183640.4377202703690.3299425783170.310374266397-0.0141724260961-0.02005871651190.0405571085607-0.0176767694466-0.03143954658610.07228124730130.00651203319733-0.007437491910570.0553154417930.1695531377010.0154175863422-0.007250400745880.154792887970.01232845076410.16697100028518.46238782191.5342528211513.410088405
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 69 )20 - 691 - 50
22chain 'A' and (resid 70 through 166 )70 - 16651 - 136
33chain 'A' and (resid 167 through 242 )167 - 242137 - 212
44chain 'A' and (resid 243 through 386 )243 - 386213 - 356

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