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- PDB-7aqx: Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in comp... -

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Basic information

Entry
Database: PDB / ID: 7aqx
TitleCo-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB9)
Components
  • Nanobody VSG2(NB9)
  • Variant surface glycoprotein MITAT 1.2
KeywordsMEMBRANE PROTEIN / Variant surface Glycoprotein / Epitope Mapping / Immune Evasion
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 / CITRIC ACID / Variant surface glycoprotein MITAT 1.2
Function and homology information
Biological speciesLama glama (llama)
Trypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsStebbins, C.E. / Hempelmann, A.
CitationJournal: Cell Rep / Year: 2021
Title: Nanobody-mediated macromolecular crowding induces membrane fission and remodeling in the African trypanosome.
Authors: Hempelmann, A. / Hartleb, L. / van Straaten, M. / Hashemi, H. / Zeelen, J.P. / Bongers, K. / Papavasiliou, F.N. / Engstler, M. / Stebbins, C.E. / Jones, N.G.
History
DepositionOct 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 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 MITAT 1.2
B: Variant surface glycoprotein MITAT 1.2
C: Nanobody VSG2(NB9)
D: Nanobody VSG2(NB9)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7079
Polymers109,1334
Non-polymers1,5735
Water16,664925
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Complex can be verified by FPLC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-47 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.088, 95.565, 123.721
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

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


Mass: 38844.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Glycosylated at N289 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: Antibody Nanobody VSG2(NB9)


Mass: 15722.019 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bound to Variant Surface Glycoprotein VSG2 / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): wk6

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 928 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H8O7
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 925 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.26 % / Description: rod-like shape with pyramidal endings.
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 1500, 0.1 M citrate

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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: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.499→47.782 Å / Num. obs: 11913750 / % possible obs: 99.18 % / Redundancy: 67.3 % / CC1/2: 0.992 / Net I/σ(I): 51.47
Reflection shellResolution: 1.499→1.553 Å / Num. unique obs: 17100 / CC1/2: 0.594

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Cootmodel building
MOSFLMdata processing
PHENIX1.15.2_3472phasing
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSG, 5lhr(ChainB)

1vsg

5lhr


Resolution: 1.499→47.782 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 8847 5 %
Rwork0.1641 168156 -
obs0.1654 177003 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.65 Å2 / Biso mean: 33.5241 Å2 / Biso min: 15.82 Å2
Refinement stepCycle: final / Resolution: 1.499→47.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 195 925 7847
Biso mean--39.66 39.96 -
Num. residues----939
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4993-1.51630.28512730.2626522293
1.5163-1.53410.28842900.2464551799
1.5341-1.55290.2842900.24550899
1.5529-1.57250.27272890.2249552098
1.5725-1.59320.25132900.2158552199
1.5932-1.6150.28222910.2116555499
1.615-1.63810.24262930.2003553299
1.6381-1.66260.27082900.2056552699
1.6626-1.68850.26162930.2023554999
1.6885-1.71620.24422930.185555499
1.7162-1.74580.22142910.1761558999
1.7458-1.77760.23072910.1545553399
1.7776-1.81180.20072940.1524558899
1.8118-1.84870.21022930.1502556299
1.8487-1.88890.20462950.1475559999
1.8889-1.93290.20492940.1495574100
1.9329-1.98120.20852960.15025615100
1.9812-2.03480.20262950.15035619100
2.0348-2.09470.17442960.14665620100
2.0947-2.16230.16992950.14235612100
2.1623-2.23960.1742970.13595651100
2.2396-2.32920.16582960.13125636100
2.3292-2.43520.16612990.13825663100
2.4352-2.56360.17042970.14035655100
2.5636-2.72420.17263000.14795680100
2.7242-2.93450.18483000.15925706100
2.9345-3.22980.19593000.17425699100
3.2298-3.6970.17783030.1675746100
3.697-4.65720.173050.15275794100
4.6572-47.7820.20693180.20056012100

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