+Open data
-Basic information
Entry | Database: PDB / ID: 1kjm | ||||||
---|---|---|---|---|---|---|---|
Title | TAP-A-associated rat MHC class I molecule | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / peptide-MHC complex / heterodimer / extracellular domain | ||||||
Function / homology | Function and homology information Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Neutrophil degranulation / response to cadmium ion / 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 ...Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Neutrophil degranulation / response to cadmium ion / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / 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 / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / response to xenobiotic stimulus / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / structural molecule activity / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Rudolph, M.G. / Stevens, J. / Speir, J.A. / Trowsdale, J. / Butcher, G.W. / Joly, E. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B. Authors: Rudolph, M.G. / Stevens, J. / Speir, J.A. / Trowsdale, J. / Butcher, G.W. / Joly, E. / Wilson, I.A. #1: Journal: Immunity / Year: 2001 Title: Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa Authors: Speir, J.A. / Stevens, J.S. / Joly, E. / Butcher, G.W. / Wilson, I.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kjm.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kjm.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kjm_validation.pdf.gz | 451.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kjm_full_validation.pdf.gz | 466.5 KB | Display | |
Data in XML | 1kjm_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1kjm_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/1kjm ftp://data.pdbj.org/pub/pdb/validation_reports/kj/1kjm | HTTPS FTP |
-Related structure data
Related structure data | 1kjvC 1ed3S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 33326.961 Da / Num. of mol.: 1 Fragment: extracellular domain, residues 25-300, numbered 1-276, plus C-terminal his tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P16391 |
---|---|
#2: Protein | Mass: 11783.478 Da / Num. of mol.: 1 / Fragment: residues 21-119, numbered 1-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P07151 |
#3: Protein/peptide | Mass: 924.979 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide was derived from biochemical binding data. |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2M (NH4)2SO4, 1% glycerol, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999 |
Radiation | Monochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→19.8 Å / Num. obs: 22313 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.76 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.38 % / Mean I/σ(I) obs: 1.86 / Num. unique all: 2120 / Rsym value: 0.423 / % possible all: 92 |
Reflection | *PLUS Redundancy: 2.8 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 92 % / Redundancy: 2.4 % / Num. unique obs: 2120 / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ED3 MOLECULE 1 Resolution: 2.35→19.8 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.91 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.686 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→19.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.412 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 19.8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.246 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.41 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.359 |