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- EMDB-30199: Cryo-EM reconstruction of PEGylated full-length NOD2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30199
TitleCryo-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 / antibacterial innate immune response / positive regulation of humoral immune response mediated by circulating immunoglobulin / maintenance of gastrointestinal epithelium / positive regulation of mitophagy / positive regulation of xenophagy / xenophagy / positive regulation of protein K63-linked ubiquitination / positive regulation of type 2 immune response / positive regulation of B cell activation / cellular response to muramyl dipeptide / CARD domain binding / cellular response to peptidoglycan / peptidoglycan binding / negative regulation of interleukin-12 production / positive regulation of cytokine production involved in inflammatory response / nucleotide-binding oligomerization domain containing 2 signaling pathway / 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 / response to exogenous dsRNA / positive regulation of Notch signaling pathway / positive regulation of interleukin-17 production / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interleukin-10 production / response to muramyl dipeptide / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of phagocytosis / phagocytic vesicle / phagocytosis / JNK cascade / negative regulation of inflammatory response to antigenic stimulus / ERK1 and ERK2 cascade / Hsp70 protein binding / response to endoplasmic reticulum stress / detection of bacterium / positive regulation of interleukin-12 production / innate immune response in mucosa / ubiquitin binding / positive regulation of interleukin-1 beta production / positive regulation of epithelial cell proliferation / positive regulation of interleukin-8 production / ADP binding / establishment of localization in cell / positive regulation of JNK cascade / Hsp90 protein binding / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / actin binding / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / 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
NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Leucine rich repeat, ribonuclease inhibitor type / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine Rich repeat / CARD domain ...NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / Leucine rich repeat, ribonuclease inhibitor type / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Leucine Rich repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nucleotide-binding oligomerization domain-containing protein 2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang Z / Ohto U / Shimizu T
CitationJournal: 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
DepositionApr 8, 2020-
Header (metadata) releaseJun 16, 2021-
Map releaseJun 16, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30199.png

Downloads & links

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Map

FileDownload / File: emd_30199.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.14125 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.08931723 - 0.13156876
Average (Standard dev.)-2.020651e-05 (±0.004678156)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 182.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141251.141251.14125
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z182.600182.600182.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-250-250-250
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0890.132-0.000

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Supplemental data

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Sample components

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Entire : NOD2 complexed with ADP

EntireName: NOD2 complexed with ADP
Components
  • Complex: NOD2 complexed with ADP

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Supramolecule #1: NOD2 complexed with ADP

SupramoleculeName: NOD2 complexed with ADP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143074

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