+Open data
-Basic information
Entry | Database: PDB / ID: 4z7v | |||||||||
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Title | L3-12 complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNE RECEPTOR-LIGAND COMPLEX | |||||||||
Function / homology | Function and homology information nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Triticum aestivum (bread wheat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Petersen, J. / Rossjohn, J. / Reid, H.H. / Koning, F. | |||||||||
Citation | Journal: J Immunol. / Year: 2015 Title: Determinants of Gliadin-Specific T Cell Selection in Celiac Disease. Authors: Petersen, J. / van Bergen, J. / Loh, K.L. / Kooy-Winkelaar, Y. / Beringer, D.X. / Thompson, A. / Bakker, S.F. / Mulder, C.J. / Ladell, K. / McLaren, J.E. / Price, D.A. / Rossjohn, J. / Reid, H.H. / Koning, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z7v.cif.gz | 655.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z7v.ent.gz | 540.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/4z7v ftp://data.pdbj.org/pub/pdb/validation_reports/z7/4z7v | HTTPS FTP |
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-Related structure data
Related structure data | 4z7uSC 4z7wC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-MHC class II HLA-DQ- ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 21882.221 Da / Num. of mol.: 2 / Fragment: UNP residues 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q30069 #2: Protein | Mass: 24484.211 Da / Num. of mol.: 2 / Fragment: UNP residues 1-192 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19707 |
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-T-CELL RECEPTOR, L3-12 ... , 2 types, 4 molecules EGFH
#3: Protein | Mass: 22850.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 #4: Protein | Mass: 27475.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 |
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-Protein/peptide / Non-polymers , 2 types, 337 molecules IJ
#5: Protein/peptide | Mass: 1803.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18573*PLUS #9: Water | ChemComp-HOH / | |
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-Sugars , 3 types, 4 molecules
#6: Polysaccharide | alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: Polysaccharide | alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#8: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.28 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000 PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→74.14 Å / Num. obs: 61285 / % possible obs: 98.28 % / Redundancy: 2.6 % / Biso Wilson estimate: 63.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.38 |
Reflection shell | Resolution: 2.65→2.745 Å / Redundancy: 2.62 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.21 / % possible all: 97.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z7U Resolution: 2.65→74.14 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.886 / SU R Cruickshank DPI: 0.601 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.523 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.278
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Displacement parameters | Biso mean: 61.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.362 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→74.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.72 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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