- PDB-2d31: Crystal structure of disulfide-linked HLA-G dimer -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2d31
Title
Crystal structure of disulfide-linked HLA-G dimer
Components
9-mer peptide from Histone H2A
Beta-2-microglobulin
HLA class I histocompatibility antigen, alpha chain G
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 / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / negative regulation of immune response / positive regulation of T cell tolerance induction / negative regulation of G0 to G1 transition ...peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / negative regulation of immune response / positive regulation of T cell tolerance induction / negative regulation of G0 to G1 transition / XY body / chromatin-protein adaptor activity / protein localization to site of double-strand break / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / positive regulation of macrophage cytokine production / positive regulation of regulatory T cell differentiation / response to ionizing radiation / CD8 receptor binding / protein homotrimerization / site of DNA damage / protection from natural killer cell mediated cytotoxicity / positive regulation of endothelial cell apoptotic process / 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 defense response / Replacement of protamines by nucleosomes in the male pronucleus / Packaging Of Telomere Ends / negative regulation of T cell proliferation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of interleukin-12 production / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / positive regulation of DNA repair / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / negative regulation of angiogenesis / DNA methylation / negative regulation of receptor binding / DNA damage checkpoint signaling / early endosome lumen / Condensation of Prophase Chromosomes / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / condensed nuclear chromosome / replication fork / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transferrin transport / PRC2 methylates histones and DNA / cellular response to iron ion / Regulation of endogenous retroelements by KRAB-ZFP proteins / meiotic cell cycle / Defective pyroptosis / lumenal side of endoplasmic reticulum membrane / male germ cell nucleus / double-strand break repair via homologous recombination / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / Transcriptional regulation by small RNAs / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / Formation of the beta-catenin:TCF transactivating complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / T cell mediated cytotoxicity / G2/M DNA damage checkpoint / antigen processing and presentation of endogenous peptide antigen via MHC class I / NoRC negatively regulates rRNA expression / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / positive regulation of T cell activation / peptide antigen binding / Meiotic recombination / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
Histone H2AX / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin Similarity search - Component
A: HLA class I histocompatibility antigen, alpha chain G B: Beta-2-microglobulin C: 9-mer peptide from Histone H2A D: HLA class I histocompatibility antigen, alpha chain G E: Beta-2-microglobulin F: 9-mer peptide from Histone H2A
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi