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Open data
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Basic information
Entry | Database: PDB / ID: 8tq8 | ||||||
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Title | Crystal structure of Fab.34.5.8 in complex with MHC-I (H2-Dd) | ||||||
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![]() | IMMUNE SYSTEM / histocompatibility complex class I / MHC-I / immune response / immune system Fab / antibody / anti-MHC antibody / cancer tumor | ||||||
Function / homology | ![]() Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Binding and entry of HIV virion / beta-2-microglobulin binding / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / Neutrophil degranulation / host cell endosome membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / actin filament organization / lumenal side of endoplasmic reticulum membrane / Assembly Of The HIV Virion / peptide binding / 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 / regulation of iron ion transport / Budding and maturation of HIV virion / 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 / 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 / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / symbiont entry into host cell / immune response / external side of plasma membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / signaling receptor binding / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, J. / Boyd, L.F. / Natarajan, K. / Margulies, D.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. Authors: Boyd, L.F. / Jiang, J. / Ahmad, J. / Natarajan, K. / Margulies, D.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 526.3 KB | Display | ![]() |
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PDB format | ![]() | 394.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8tq7C ![]() 8tq9C ![]() 8tqaC ![]() 5weuS ![]() 8tq4 ![]() 8tq5 ![]() 8tq6 C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 31819.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Mutation: A85D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules PE
#3: Protein/peptide | Mass: 1075.265 Da / Num. of mol.: 2 / Fragment: HV1: HIV-1 P18-I10 (UNP residues 311-320) / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Antibody , 2 types, 4 molecules HFLG
#4: Antibody | Mass: 23325.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Antibody | Mass: 24207.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 131 molecules ![](data/chem/img/GOL.gif)
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![](data/chem/img/HOH.gif)
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#6: Chemical | ChemComp-GOL / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 18% PEG4000, 0.1 M MES, pH 6.0, 0.12 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→87.09 Å / Num. obs: 54120 / % possible obs: 97.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.76 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.085 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.69→2.8 Å / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5458 / CC1/2: 0.565 / CC star: 0.85 / Rpim(I) all: 0.455 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5WEU Resolution: 2.69→87.09 Å / Cross valid method: FREE R-VALUE / σ(F): 154.07 / Phase error: 23.426 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→87.09 Å
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Refine LS restraints |
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LS refinement shell |
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