[English] 日本語
![](img/lk-miru.gif)
- PDB-1vac: MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1vac | ||||||
---|---|---|---|---|---|---|---|
Title | MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND CHICKEN OVALBUMIN | ||||||
![]() |
| ||||||
![]() | COMPLEX (MHC I/PEPTIDE) / HISTOCOMPATIBILITY ANTIGEN / CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX / MHC I / COMPLEX (MHC I-PEPTIDE) COMPLEX | ||||||
Function / homology | ![]() intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / response to steroid hormone / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / embryo development ending in birth or egg hatching / ER-Phagosome pathway ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / response to steroid hormone / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / embryo development ending in birth or egg hatching / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to corticosterone / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / monoatomic ion transport / phagocytic vesicle / Neutrophil degranulation / early endosome lumen / 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 / Neutrophil degranulation / response to progesterone / lumenal side of endoplasmic reticulum membrane / 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 / 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 / response to estrogen / 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 / protease binding / protein homotetramerization / intracellular iron ion homeostasis / vesicle / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / signaling receptor binding / calcium ion binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Fremont, D.H. / Wilson, I.A. | ||||||
![]() | ![]() Title: Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Authors: Fremont, D.H. / Stura, E.A. / Matsumura, M. / Peterson, P.A. / Wilson, I.A. #1: ![]() Title: Crystal Structures of Two Viral Peptides in Complex with Murine Mhc Class I H-2Kb Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A. #2: ![]() Title: Emerging Principles for the Recognition of Peptide Antigens by Mhc Class I Molecules Authors: Matsumura, M. / Fremont, D.H. / Peterson, P.A. / Wilson, I.A. #3: ![]() Title: Crystallization of Murine Major Histocompatibility Complex Class I H-2Kb with Single Peptides Authors: Stura, E.A. / Matsumura, M. / Fremont, D.H. / Saito, Y. / Peterson, P.A. / Wilson, I.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 964.137 Da / Num. of mol.: 1 / Fragment: RESIDUES 257 - 264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS Density % sol: 62 % | |||||||||||||||
Crystal grow | *PLUS Temperature: 17.0 ℃ / pH: 6.2 / Method: unknown / Details: used macroseeding | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Wavelength: 1.5418 |
---|---|
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 18598 / % possible obs: 93.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. measured all: 43371 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→6 Å / σ(F): 2 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |