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- PDB-7p5d: Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (s... -

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Basic information

Entry
Database: PDB / ID: 7p5d
TitleVariant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (serine 317 and 319 to alanine)
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 / Variant surface glycoprotein
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity_src_gen / pdbx_nonpoly_scheme
Item: _atom_site_anisotrop.id / _entity_src_gen.pdbx_gene_src_gene ..._atom_site_anisotrop.id / _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 23, 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)54,9752
Polymers53,9021
Non-polymers1,0731
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint23 kcal/mol
Surface area16660 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)164,9266
Polymers161,7073
Non-polymers3,2193
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14720 Å2
ΔGint19 kcal/mol
Surface area40880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.183, 129.183, 129.183
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-803-

HOH

21A-828-

HOH

31A-840-

HOH

41A-845-

HOH

51A-846-

HOH

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Components

#1: Protein Variant surface glycoprotein


Mass: 53902.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Both Serine317 and Serine319 from the wild type VSG3 sequence have been mutated to alanine.
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES153.14, Tb427.BES65.13 / Cell line (production host): VSG3SSAA / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 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: 1.42→40.85 Å / Num. obs: 66947 / % possible obs: 99.95 % / Redundancy: 20 % / Biso Wilson estimate: 20.1 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.1164 / Rpim(I) all: 0.02664 / Rrim(I) all: 0.1195 / Net I/σ(I): 20.08
Reflection shellResolution: 1.42→1.474 Å / Redundancy: 19.1 % / Rmerge(I) obs: 2.767 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 6654 / CC1/2: 0.455 / CC star: 0.791 / Rpim(I) all: 0.6492 / Rrim(I) all: 2.843 / % possible all: 99.64

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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: 1.42→40.85 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2845
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 3346 5 %
Rwork0.1742 63575 -
obs0.1751 66947 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.97 Å2
Refinement stepCycle: LAST / Resolution: 1.42→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 72 246 2915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00572736
X-RAY DIFFRACTIONf_angle_d0.96673726
X-RAY DIFFRACTIONf_chiral_restr0.0677458
X-RAY DIFFRACTIONf_plane_restr0.006481
X-RAY DIFFRACTIONf_dihedral_angle_d4.9161433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.3371370.31122597X-RAY DIFFRACTION99.17
1.44-1.460.30681400.28692656X-RAY DIFFRACTION100
1.46-1.490.30451380.27352629X-RAY DIFFRACTION99.96
1.49-1.510.27081390.25182629X-RAY DIFFRACTION99.96
1.51-1.540.26311380.2572624X-RAY DIFFRACTION100
1.54-1.570.25811380.23212628X-RAY DIFFRACTION100
1.57-1.60.24281390.21032644X-RAY DIFFRACTION100
1.6-1.630.2431390.19442627X-RAY DIFFRACTION100
1.63-1.660.23191390.19372640X-RAY DIFFRACTION100
1.66-1.70.22741360.18392593X-RAY DIFFRACTION100
1.7-1.750.19331400.17552669X-RAY DIFFRACTION100
1.75-1.790.19421390.17112632X-RAY DIFFRACTION100
1.79-1.850.21211400.1792651X-RAY DIFFRACTION100
1.85-1.90.19851370.18372610X-RAY DIFFRACTION100
1.91-1.970.21841390.17492641X-RAY DIFFRACTION100
1.97-2.050.16941400.15722658X-RAY DIFFRACTION100
2.05-2.150.18341400.15722674X-RAY DIFFRACTION100
2.15-2.260.17981400.15892641X-RAY DIFFRACTION100
2.26-2.40.18031390.162653X-RAY DIFFRACTION99.96
2.4-2.580.20271410.16092675X-RAY DIFFRACTION100
2.59-2.840.19851390.16372649X-RAY DIFFRACTION100
2.85-3.260.1751420.17122686X-RAY DIFFRACTION100
3.26-4.10.16841410.16152683X-RAY DIFFRACTION100
4.11-45.670.1761460.17412786X-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)
11.38001608671.557234077881.451784444291.768040110231.703390133581.791070259830.014010016499-0.00746640277287-0.126210499673-0.03792822684250.0648693235712-0.161327346305-0.0559337716144-0.0130405808322-0.0987277191450.1816499016040.01593753668020.004204766762050.166143047210.002558733292050.19657250369818.467989251823.30891127255.59559070569
22.56975434354-1.01327753544-1.231485035113.9809670131-0.005759728631231.86648056715-0.003835671567230.1470410901470.128407878328-0.4103984969450.1418679166060.1102745341260.0281075161659-0.176853332157-0.1394566753840.214206939547-0.0265129583305-0.0229165336850.2264569143440.02823064911450.131339041668-4.363690175638.36585708779-23.2997824849
33.918439997863.022202618953.540254031083.894792530374.357269330536.31852199111-0.258480173194-0.04592659506480.311539233624-0.3706108115-0.103659620280.368186329345-0.16712213257-0.1372824166110.2994551041440.1938040804350.0145094016888-0.02494838040870.1508229754250.02795827888620.164229712571-4.228701370684.57055930758-11.7979418481
41.011127232731.109270433220.7266963762382.539902896711.441774903812.10162328780.0260637236730.04389370305740.0121316855689-0.0965175482957-0.01654022021010.0279213244809-0.070608609502-0.04651326775560.02079672012840.1373408566130.01836437722520.01038739279640.1333132181550.01570474275540.15204575897223.620032664642.96879037810.6043402014
50.4771073675450.2200321319130.094784278170.810072972532-0.08392247455860.6419339691260.04688753664720.01034689478790.02906719537440.103973395651-0.0125285208088-0.01111761784960.0140561578804-0.038004463562-0.04026628577950.1995609860840.01005741357370.002953753831460.1679044685850.008207000861410.17730302441124.623775259839.880022506820.6420582579
61.44264710123.732930761512.178174064779.693923951965.798071670633.725993304860.0869344623949-0.0327757028524-0.05307523203510.0851102446766-0.0739631180952-0.1064178304940.114822139371-0.0690748095435-0.02971749566750.1961225460690.00694312494243-0.01176430116050.176090453572-0.001550483459040.1939625541696.249549940429.47900348736-1.83778583355
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 - 53
22chain 'A' and (resid 70 through 135 )70 - 13554 - 111
33chain 'A' and (resid 136 through 166 )136 - 166112 - 143
44chain 'A' and (resid 167 through 242 )167 - 242144 - 220
55chain 'A' and (resid 243 through 340 )243 - 340221 - 318
66chain 'A' and (resid 341 through 389 )341 - 389319 - 367

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