+Open data
-Basic information
Entry | Database: PDB / ID: 2d31 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of disulfide-linked HLA-G dimer | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/CELL CYCLE / MHC class I / IMMUNE SYSTEM-CELL CYCLE COMPLEX | ||||||
Function / homology | Function and homology information peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / chromatin-protein adaptor activity ...peripheral B cell tolerance induction / positive regulation of tolerance induction / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / positive regulation of T cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / chromatin-protein adaptor activity / negative regulation of G0 to G1 transition / negative regulation of immune response / positive regulation of endothelial cell apoptotic process / XY body / protein localization to site of double-strand break / positive regulation of regulatory T cell differentiation / filopodium membrane / positive regulation of macrophage cytokine production / response to ionizing radiation / CD8 receptor binding / protein homotrimerization / site of DNA damage / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protection from natural killer cell mediated cytotoxicity / condensed nuclear chromosome / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of DNA repair / Packaging Of Telomere Ends / cellular defense response / meiotic cell cycle / male germ cell nucleus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of angiogenesis / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / positive regulation of interleukin-12 production / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / Defective pyroptosis / early endosome lumen / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / DNA damage checkpoint signaling / 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 / replication fork / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / cellular response to iron ion / Endosomal/Vacuolar pathway / Transcriptional regulation by small RNAs / lumenal side of endoplasmic reticulum membrane / Transcriptional regulation of granulopoiesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / cellular response to iron(III) ion / NoRC negatively regulates rRNA expression / double-strand break repair via homologous recombination / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / B-WICH complex positively regulates rRNA expression / 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 / heterochromatin formation / cellular senescence / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / cellular response to gamma radiation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / MHC class I protein complex / cerebral cortex development / multicellular organismal-level iron ion homeostasis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Shiroishi, M. / Kuroki, K. / Ose, T. / Rasubala, L. / Shiratori, I. / Arase, H. / Tsumoto, K. / Kumagai, I. / Kohda, D. / Maenaka, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Efficient Leukocyte Ig-like Receptor Signaling and Crystal Structure of Disulfide-linked HLA-G Dimer Authors: Shiroishi, M. / Kuroki, K. / Ose, T. / Rasubala, L. / Shiratori, I. / Arase, H. / Tsumoto, K. / Kumagai, I. / Kohda, D. / Maenaka, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2d31.cif.gz | 145.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2d31.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 2d31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d31_validation.pdf.gz | 466.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2d31_full_validation.pdf.gz | 494.7 KB | Display | |
Data in XML | 2d31_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 2d31_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/2d31 ftp://data.pdbj.org/pub/pdb/validation_reports/d3/2d31 | HTTPS FTP |
-Related structure data
Related structure data | 1mheS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31902.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17693 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1148.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P16104 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: CAPS, PEG8000, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 12897 / % possible obs: 83.8 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1162 / % possible all: 77.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MHE Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.799 / SU B: 30.757 / SU ML: 0.526 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.459 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
|