- EMDB-30199: Cryo-EM reconstruction of PEGylated full-length NOD2 -
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Basic information
Entry
Database: EMDB / ID: EMD-30199
Title
Cryo-EM reconstruction of PEGylated full-length NOD2
Map data
Sample
Complex: NOD2 complexed with ADP
Function / homology
Function and homology information
biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / positive regulation of dendritic cell antigen processing and presentation / host-mediated regulation of intestinal microbiota composition / intestinal stem cell homeostasis ...biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / positive regulation of dendritic cell antigen processing and presentation / host-mediated regulation of intestinal microbiota composition / intestinal stem cell homeostasis / negative regulation of toll-like receptor 2 signaling pathway / regulation of appetite / toll-like receptor 2 signaling pathway / negative regulation of macrophage cytokine production / negative regulation of macrophage apoptotic process / positive regulation of humoral immune response mediated by circulating immunoglobulin / antibacterial innate immune response / maintenance of gastrointestinal epithelium / positive regulation of mitophagy / positive regulation of xenophagy / xenophagy / positive regulation of B cell activation / positive regulation of type 2 immune response / positive regulation of protein K63-linked ubiquitination / positive regulation of stress-activated MAPK cascade / cellular response to muramyl dipeptide / CARD domain binding / cellular response to peptidoglycan / peptidoglycan binding / negative regulation of interleukin-12 production / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage cytokine production / pattern recognition receptor activity / negative regulation of interleukin-2 production / temperature homeostasis / extrinsic component of plasma membrane / positive regulation of Notch signaling pathway / response to exogenous dsRNA / positive regulation of interleukin-17 production / positive regulation of nitric-oxide synthase biosynthetic process / response to muramyl dipeptide / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / phagocytosis / detection of bacterium / stress-activated MAPK cascade / positive regulation of phagocytosis / JNK cascade / negative regulation of inflammatory response to antigenic stimulus / Hsp70 protein binding / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / phagocytic vesicle / response to endoplasmic reticulum stress / innate immune response in mucosa / positive regulation of interleukin-1 beta production / ubiquitin binding / positive regulation of interleukin-8 production / positive regulation of epithelial cell proliferation / establishment of localization in cell / positive regulation of JNK cascade / Hsp90 protein binding / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / actin binding / basolateral plasma membrane / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / defense response to bacterium / protein-containing complex binding / protein kinase binding / Golgi apparatus / cell surface / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / ATP binding / cytosol Similarity search - Function
Journal: Structure / Year: 2021 Title: Improving particle quality in cryo-EM analysis using a PEGylation method. Authors: Zhikuan Zhang / Hideki Shigematsu / Toshiyuki Shimizu / Umeharu Ohto / Abstract: Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation ...Cryo-electron microscopy (cryo-EM) is widely used for structural biology studies and has been developed extensively in recent years. However, its sample vitrification process is a major limitation because it causes severe particle aggregation and/or denaturation. This effect is thought to occur because particles tend to stick to the "deadly" air-water interface during vitrification. Here, we report a method for PEGylation of proteins that can efficiently protect particles against such problems during vitrification. This method alleviates the laborious process of fine-tuning the vitrification conditions, allowing for analysis of samples that would otherwise be discarded.
History
Deposition
Apr 8, 2020
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Header (metadata) release
Jun 16, 2021
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Map release
Jun 16, 2021
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Update
Oct 20, 2021
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Current status
Oct 20, 2021
Processing site: PDBj / Status: Released
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Structure visualization
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Surface view with section colored by density value
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