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- PDB-7ar0: Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ar0 | ||||||
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Title | Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB19) | ||||||
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![]() | MEMBRANE PROTEIN / Variant surface Glycoprotein / Epitope Mapping / Immune Evasion | ||||||
Function / homology | Variant 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![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stebbins, C.E. / Hempelmann, A. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7aqxC ![]() 7aqyC ![]() 7aqzC ![]() 1vsgS ![]() 5lhrS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38844.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Glycosylated at N289 / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 13746.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#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 Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.33 Å3/Da / Density % sol: 71.59 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ADA pH 6.5, 2 M Ammonium Sulfate, 0.1 MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.139→2.216 Å / Num. unique obs: 4971 / CC1/2: 0.591 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VSG, 5lhr(ChainB) 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.52 Å2 / Biso mean: 35.8144 Å2 / Biso min: 19.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.139→75.726 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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