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Yorodumi- PDB-6id4: Defining the structural basis for human alloantibody binding to h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6id4 | |||||||||
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Title | Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Lescar, J. / Wong, Y.H. / Liew, C.W. / Gu, Y. / MacAry, P.A. | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01. Authors: Gu, Y. / Wong, Y.H. / Liew, C.W. / Chan, C.E.Z. / Murali, T.M. / Yap, J. / Too, C.T. / Purushotorman, K. / Hamidinia, M. / El Sahili, A. / Goh, A.T.H. / Teo, R.Z.C. / Wood, K.J. / Hanson, B. ...Authors: Gu, Y. / Wong, Y.H. / Liew, C.W. / Chan, C.E.Z. / Murali, T.M. / Yap, J. / Too, C.T. / Purushotorman, K. / Hamidinia, M. / El Sahili, A. / Goh, A.T.H. / Teo, R.Z.C. / Wood, K.J. / Hanson, B.J. / Gascoigne, N.R.J. / Lescar, J. / Vathsala, A. / MacAry, P.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6id4.cif.gz | 665.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6id4.ent.gz | 548.8 KB | Display | PDB format |
PDBx/mmJSON format | 6id4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6id4 ftp://data.pdbj.org/pub/pdb/validation_reports/id/6id4 | HTTPS FTP |
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-Related structure data
Related structure data | 1w72S S: Starting model for refinement |
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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
-Protein , 2 types, 4 molecules AEBF
#1: Protein | Mass: 31986.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: F6IQY1 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules TU
#5: Protein/peptide | Mass: 1013.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
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-Antibody , 2 types, 4 molecules CHDL
#3: Antibody | Mass: 23629.564 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Antibody | Mass: 23642.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 3 types, 813 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-PEG / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1,4-Dioxane, Tris pH 8.2, Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→48.69 Å / Num. obs: 79954 / % possible obs: 96.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 68.79 Å2 / CC1/2: 0.98 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.39→2.41 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.36 / Num. unique obs: 12545 / CC1/2: 0.56 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W72 Resolution: 2.4→45.78 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.353 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.247
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Displacement parameters | Biso mean: 61.53 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→45.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 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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