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- PDB-7aqy: 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: 7aqy | ||||||
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Title | Co-Crystal Structure of Variant Surface Glycoprotein VSG2 in complex with Nanobody VSG2(NB11) | ||||||
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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. / VanStraaten, M. | ||||||
![]() | ![]() 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 | ![]() | 377.6 KB | Display | ![]() |
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PDB format | ![]() | 306 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aqxC ![]() 7aqzC ![]() 7ar0C ![]() 1vsgS ![]() 5lhrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38844.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Glycosylated at N289 / Source: (natural) ![]() ![]() #2: Antibody | Mass: 14486.022 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.44 % / Description: rod |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Imidazole, 19% PEG 1500 |
-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: 1.9→54.024 Å / Num. obs: 67339 / % possible obs: 99.78 % / Redundancy: 10.8 % / CC1/2: 0.987 / Net I/σ(I): 14.76 |
Reflection shell | Resolution: 1.9→1.968 Å / Num. unique obs: 6654 / CC1/2: 0.187 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VSG, 5lhr(chainB) Resolution: 1.9→54.024 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29 / 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: 78.59 Å2 / Biso mean: 34.793 Å2 / Biso min: 15.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→54.024 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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