[English] 日本語
Yorodumi
- EMDB-6458: Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Revea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6458
TitleCryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization
Map data
SampleNAIP2/NLRC4 inflammasome, 11-fold disk
  • NLR family CARD domain-containing protein 4
  • NLR family, apoptosis inhibitory protein 2
KeywordsInflammasome / NLRC4 / NAIP2
Function / homology
Function and homology information


pyroptosis / interleukin-1 beta secretion / IPAF inflammasome complex / regulation of cysteine-type endopeptidase activity involved in apoptotic process / detection of bacterium / activation of innate immune response / activation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / regulation of apoptotic process / positive regulation of NF-kappaB transcription factor activity ...pyroptosis / interleukin-1 beta secretion / IPAF inflammasome complex / regulation of cysteine-type endopeptidase activity involved in apoptotic process / detection of bacterium / activation of innate immune response / activation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / regulation of apoptotic process / positive regulation of NF-kappaB transcription factor activity / inflammatory response / positive regulation of apoptotic process / defense response to bacterium / apoptotic process / innate immune response / protein homodimerization activity / ATP binding / identical protein binding / cytosol
NACHT nucleoside triphosphatase / NLR family CARD domain-containing protein 4 / CARD domain / NLRC4, helical domain / Leucine-rich repeat domain superfamily / Death-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
NLR family CARD domain-containing protein 4
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsZhang L / Chen S / Ruan J / Wu J / Tong AB / Yin Q / Li Y / David L / Lu A / Wang WL / Marks C / Ouyang Q / Zhang X / Mao Y / Wu H
CitationJournal: Science / Year: 2015
Title: Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.
Authors: Liman Zhang / Shuobing Chen / Jianbin Ruan / Jiayi Wu / Alexander B Tong / Qian Yin / Yang Li / Liron David / Alvin Lu / Wei Li Wang / Carolyn Marks / Qi Ouyang / Xinzheng Zhang / Youdong Mao / Hao Wu /
Abstract: The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the ...The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo-electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes.
Validation ReportPDB-ID: 3jbl

SummaryFull reportAbout validation report
History
Current status-Processing site: RCSB / Status: Released
DepositionSep 5, 2015-
Header (metadata) releaseOct 14, 2015-
Map releaseOct 21, 2015-
UpdateNov 4, 2015-

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3jbl
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3jbl
  • Surface level: 0.0045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_6458.map.gz / Format: CCP4 / Size: 335 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 385.28 Å
0.86 Å/pix.
x 448 pix.
= 385.28 Å
0.86 Å/pix.
x 448 pix.
= 385.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.0045 / Movie #1: 0.0045
Minimum - Maximum-0.0079744 - 0.01165745
Average (Standard dev.)0.00009534 (±0.00089071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 385.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z385.280385.280385.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0080.0120.000

-
Supplemental data

-
Sample components

-
Entire NAIP2/NLRC4 inflammasome, 11-fold disk

EntireName: NAIP2/NLRC4 inflammasome, 11-fold disk
Details: The sample contains multiple oligomeric states, including 10-fold, 11-fold, and 12-fold disks.
Number of components: 2 / Oligomeric State: One NAIP2 subunit and ten NLRC subunits
MassTheoretical: 1.8 MDa / Experimental: 1.8 MDa

-
Component #1: protein, NLR family CARD domain-containing protein 4

ProteinName: NLR family CARD domain-containing protein 4 / a.k.a: NLRC4
Oligomeric Details: NLRC4 inflammasome comprises ten NLRC4 and one NAIP2
Details: One activated NAIP2 induces polymerization of NLRC4.
Number of Copies: 10 / Recombinant expression: Yes
SourceSpecies: Mus musculus (house mouse) / Strain: RAW 264.7
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Vector: pFastBac1 / Cell of expression system: Sf21 / Strain: IPLB-SF21-AE
Source (natural)Location in cell: cytosol / Cell: macrophage
Organ or tissue: Abelson murine leukemia virus-induced tumor; ascites
External referencesUniProt: NLR family CARD domain-containing protein 4

-
Component #2: protein, NLR family, apoptosis inhibitory protein 2

ProteinName: NLR family, apoptosis inhibitory protein 2 / a.k.a: NAIP2
Oligomeric Details: NLRC4 inflammasome comprises one NAIP2 and ten NLRC4
Details: One activated NAIP2 induces polymerization of NLRC4.
Recombinant expression: Yes / Number of Copies: 1
SourceSpecies: Mus musculus (house mouse) / Strain: RAW 264.7
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Vector: pFastBac1 / Cell of expression system: Sf21 / Strain: IPLB-SF21-AE
Source (natural)Location in cell: cytosol / Cell: macrophage
Organ or tissue: Abelson murine leukemia virus-induced tumor; ascites

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/mL
Buffer solution: 25 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM DTT
pH: 8
Support film400 mesh C-flat grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 103 K / Humidity: 100 % / Method: Blot for one second before plunging

-
Electron microscopy imaging

ImagingMicroscope: OTHER / Date: Apr 1, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 21000 X (nominal), 28736 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 21,000 times magnification.
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 79.5 (79.5 - 80 K)
CameraDetector: GATAN K2 (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 9113 / Sampling size: 5 µm / Bit depth: 8
Details: average of 36 frames recorded by the direct electron detector

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C12 (12 fold cyclic) / Number of projections: 75114
3D reconstructionAlgorithm: Maximum-likelihood based projection matching / Software: Spider, EMAN2, Relion / CTF correction: Wiener-type filter / Resolution: 4.7 Å / Resolution method: FSC 0.143, gold-standard

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • 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.

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

Read more