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- EMDB-0438: Cryo-EM structure of NLRP6 PYD filament -

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Basic information

Entry
Database: EMDB / ID: 0438
TitleCryo-EM structure of NLRP6 PYD filament
Map dataNLRP6 PYD filament
SampleNLRP6 PYD
  • NACHT, LRR and PYD domains-containing protein 6
Function / homologyNACHT-NTPase domain profile. / DAPIN domain profile. / NACHT domain / PAAD/DAPIN/Pyrin domain / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Death-like domain superfamily / NACHT nucleoside triphosphatase / DAPIN domain / regulation of mucus secretion ...NACHT-NTPase domain profile. / DAPIN domain profile. / NACHT domain / PAAD/DAPIN/Pyrin domain / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Death-like domain superfamily / NACHT nucleoside triphosphatase / DAPIN domain / regulation of mucus secretion / vasopressin receptor activity / inflammasome complex / negative regulation of toll-like receptor signaling pathway / negative regulation of inflammatory response to antigenic stimulus / regulation of autophagy / response to bacterium / negative regulation of I-kappaB kinase/NF-kappaB signaling / negative regulation of ERK1 and ERK2 cascade / regulation of inflammatory response / wound healing / nuclear membrane / inflammatory response / innate immune response / ATP binding / plasma membrane / NACHT, LRR and PYD domains-containing protein 6
Function and homology information
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.7 Å resolution
AuthorsShen C / Fu TM / Wu H
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Molecular mechanism for NLRP6 inflammasome assembly and activation.
Authors: Chen Shen / Alvin Lu / Wen Jun Xie / Jianbin Ruan / Roberto Negro / Edward H Egelman / Tian-Min Fu / Hao Wu
Validation ReportPDB-ID: 6ncv

SummaryFull reportAbout validation report
DateDeposition: Dec 12, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 23, 2019 / Last update: Jan 23, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ncv
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ncv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0438.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.06 Å/pix.
= 190.8 Å
180 pix
1.06 Å/pix.
= 190.8 Å
180 pix
1.06 Å/pix.
= 190.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-0.15548103 - 0.32674178
Average (Standard dev.)0.0038273952 (0.01951139)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin0.00.00.0
Limit179.0179.0179.0
Spacing180180180
CellA=B=C: 190.79999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z190.800190.800190.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1550.3270.004

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Supplemental data

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Sample components

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Entire NLRP6 PYD

EntireName: NLRP6 PYD / Number of components: 2

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Component #1: protein, NLRP6 PYD

ProteinName: NLRP6 PYD / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, NACHT, LRR and PYD domains-containing protein 6

ProteinName: NACHT, LRR and PYD domains-containing protein 6 / Number of Copies: 21 / Recombinant expression: No
MassTheoretical: 11.931579 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C3 (3 fold cyclic) / Delta z: 13.8 Å / Delta phi: 56.8 deg.
Sample solutionSpecimen conc.: 1.5 mg/ml / pH: 7.4
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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