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- PDB-7ar0: Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in comp... -

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Basic information

Entry
Database: PDB / ID: 7ar0
TitleCo-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB19)
Components
  • Nanobody VSG2(NB19)
  • 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 / 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: 2.139 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 1.1Jul 6, 2022Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_assembly ...diffrn_source / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details ..._diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2May 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 1.3Feb 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
B: Nanobody VSG2(NB19)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1773
Polymers52,5912
Non-polymers5871
Water3,513195
1
A: Variant surface glycoprotein MITAT 1.2
B: Nanobody VSG2(NB19)
hetero molecules

A: Variant surface glycoprotein MITAT 1.2
B: Nanobody VSG2(NB19)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3556
Polymers105,1824
Non-polymers1,1732
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Unit cell
Length a, b, c (Å)141.738, 141.738, 89.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 38844.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Glycosylated at N289 / Source: (natural) Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: Antibody Nanobody VSG2(NB19)


Mass: 13746.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 4.33 Å3/Da / Density % sol: 71.59 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ADA pH 6.5, 2 M Ammonium Sulfate, 0.1 MgSO4

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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: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.139→75.726 Å / Num. obs: 50820 / % possible obs: 99.78 % / Redundancy: 26.7 % / CC1/2: 0.997 / Net I/σ(I): 8.7
Reflection shellResolution: 2.139→2.216 Å / Num. unique obs: 4971 / CC1/2: 0.591

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX3.25phasing
xia2data scaling
Cootmodel building
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSG, 5lhr(ChainB)

1vsg

5lhr


Resolution: 2.139→75.726 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2448 4.82 %
Rwork0.2058 48306 -
obs0.2071 50754 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.52 Å2 / Biso mean: 35.8144 Å2 / Biso min: 19.09 Å2
Refinement stepCycle: final / Resolution: 2.139→75.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 39 195 3872
Biso mean--46.57 38.12 -
Num. residues----484
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1394-2.1830.31011290.277277998
2.183-2.23050.28271580.26332761100
2.2305-2.28240.34641390.25392797100
2.2824-2.33950.27771620.24232761100
2.3395-2.40270.23781410.23642829100
2.4027-2.47340.27961340.23092814100
2.4734-2.55330.24021410.22672814100
2.5533-2.64450.28831310.23032814100
2.6445-2.75040.23221380.22042832100
2.7504-2.87560.21021550.22982789100
2.8756-3.02720.25541700.22682811100
3.0272-3.21690.25581640.22582833100
3.2169-3.46530.2261310.2052874100
3.4653-3.8140.22581390.17122860100
3.814-4.36580.16451350.15182892100
4.3658-5.50020.19721480.17782938100
5.5002-75.7260.25211330.21553108100

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