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Yorodumi- PDB-7p5a: Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p5a | |||||||||
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Title | Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (serine 317 to alanine), single O-linked glycosylated at Ser319 | |||||||||
Components | Variant surface glycoprotein | |||||||||
Keywords | MEMBRANE 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 / homology | Trypanosome variant surface glycoprotein, B-type, N-terminal domain / Trypanosomal VSG domain / Trypanosome variant surface glycoprotein, C-terminal / Trypanosome variant surface glycoprotein C-terminal domain / plasma membrane / alpha-D-glucopyranose / Variant surface glycoprotein Function and homology information | |||||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Gkeka, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p5a.cif.gz | 242.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p5a.ent.gz | 160.9 KB | Display | PDB format |
PDBx/mmJSON format | 7p5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/7p5a ftp://data.pdbj.org/pub/pdb/validation_reports/p5/7p5a | HTTPS FTP |
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-Related structure data
Related structure data | 7p56C 7p57C 7p59C 7p5bC 7p5dC 6elcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53918.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Serine317 from the wild type VSG3 sequence has been mutated to alanine. Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: Tb427.BES153.14, Tb427.BES65.13 / Cell line (production host): 224S317A (VSG3S317A) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: B3GVK1 |
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#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 Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-GLC / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 250mM NaCl, 100mM Tris, pH 8.2 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→54.75 Å / Num. obs: 26355 / % possible obs: 99.89 % / Redundancy: 30.8 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1179 / Rpim(I) all: 0.0209 / Rrim(I) all: 0.1198 / Net I/σ(I): 32.36 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8387 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2584 / CC1/2: 0.614 / CC star: 0.872 / Rpim(I) all: 0.3875 / Rrim(I) all: 0.9312 / % possible all: 99.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ELC Resolution: 1.95→45.75 Å / SU ML: 0.2262 / Cross valid method: FREE R-VALUE / σ(F): 1.75 / Phase error: 22.3616 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 24.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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