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- PDB-7rno: Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rno | ||||||||||||
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Title | Model of the Ac-6-FP/hpMR1/bB2m/TAPBPR complex from integrated docking, NMR and restrained MD | ||||||||||||
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![]() | IMMUNE SYSTEM / TAPBPR / MR1 / MHC-I / chaperones / adaptive immune system / antigen processing and presentation | ||||||||||||
Function / homology | ![]() ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / beta-2-microglobulin binding / T cell receptor binding / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / T cell differentiation in thymus / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | SOLUTION NMR / molecular dynamics | ||||||||||||
![]() | McShan, A.C. / Sgourakis, N.G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules. Authors: McShan, A.C. / Devlin, C.A. / Papadaki, G.F. / Sun, Y. / Green, A.I. / Morozov, G.I. / Burslem, G.M. / Procko, E. / Sgourakis, 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 | ![]() | 2.2 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
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Full document | ![]() | 625.4 KB | Display | |
Data in XML | ![]() | 142.9 KB | Display | |
Data in CIF | ![]() | 198.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 31724.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MR1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 11784.345 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 42608.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-30W / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 100 uM hpMR1 (human platform MR1), 100 uM [U-100% 12C; U-100% 15N; Ala CB, Ile CD1, Leu CD1/CD2, Val CG1/CG2] bovine beta 2 microglobulin, 300 uM TAPBPR, 90% H2O/10% D2O Details: 100 uM AILV bB2m with natural abundance hpMR1, TAPBPR and Ac-6-FP Label: ILVproS_sample2 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Details: buffer: 50 mM NaCl, 20 mM sodium phosphate pH 7.2, 10% D2O Ionic strength: 50 mM / Label: sampleconditions / pH: 7.2 / Pressure: 1.01325 bar / Temperature: 298.15 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: HADDOCK in combination with NMR derived chemical shift perturbations was used to generate the initial model of the complex. The TAP binding protein-like variant starting structure is PDB ID ...Details: HADDOCK in combination with NMR derived chemical shift perturbations was used to generate the initial model of the complex. The TAP binding protein-like variant starting structure is PDB ID 5WER chain C. The major histocompatibility complex class I-related gene protein and beta-2-microglobulin are homology modeled based on PDB ID 4PJ5 chain A and chain B. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10000 / Conformers submitted total number: 10 |