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- PDB-6ncv: Cryo-EM structure of NLRP6 PYD filament -

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Basic information

Entry
Database: PDB / ID: 6ncv
TitleCryo-EM structure of NLRP6 PYD filament
ComponentsNACHT, LRR and PYD domains-containing protein 6
KeywordsSIGNALING PROTEIN / PROTEIN FIBRIL / death domain fold / helical assembly / inflammasome
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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.7 Å resolution
AuthorsShen, C. / Fu, T.M. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Dec 12, 2018 / Release: Jan 23, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 23, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title

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Assembly

Deposited unit
A: NACHT, LRR and PYD domains-containing protein 6
B: NACHT, LRR and PYD domains-containing protein 6
C: NACHT, LRR and PYD domains-containing protein 6
D: NACHT, LRR and PYD domains-containing protein 6
E: NACHT, LRR and PYD domains-containing protein 6
F: NACHT, LRR and PYD domains-containing protein 6
G: NACHT, LRR and PYD domains-containing protein 6
H: NACHT, LRR and PYD domains-containing protein 6
I: NACHT, LRR and PYD domains-containing protein 6
J: NACHT, LRR and PYD domains-containing protein 6
K: NACHT, LRR and PYD domains-containing protein 6
L: NACHT, LRR and PYD domains-containing protein 6
M: NACHT, LRR and PYD domains-containing protein 6
N: NACHT, LRR and PYD domains-containing protein 6
O: NACHT, LRR and PYD domains-containing protein 6
P: NACHT, LRR and PYD domains-containing protein 6
Q: NACHT, LRR and PYD domains-containing protein 6
R: NACHT, LRR and PYD domains-containing protein 6
S: NACHT, LRR and PYD domains-containing protein 6
T: NACHT, LRR and PYD domains-containing protein 6
V: NACHT, LRR and PYD domains-containing protein 6


Theoretical massNumber of molelcules
Total (without water)250,56321
Polyers250,56321
Non-polymers00
Water0
1


  • idetical with deposited unit
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  • Evidence: microscopy, assay for oligomerization
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)35720
ΔGint (kcal/M)26
Surface area (Å2)85000
Helical symmetryCircular symmetry: 3 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 21 / Rise per n subunits: 13.8 Å / Rotation per n subunits: 56.8 deg.

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Components

#1: Protein/peptide ...
NACHT, LRR and PYD domains-containing protein 6 / Angiotensin II/vasopressin receptor / PYRIN-containing APAF1-like protein 5 / NLRP6


Mass: 11931.579 Da / Num. of mol.: 21 / Fragment: PYD domain (UNP residues 1-106) / Source: (gene. exp.) Homo sapiens (human) / Gene: NLRP6, NALP6, PYPAF5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59044

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: NLRP6 PYD / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 56.8 deg. / Axial rise/subunit: 13.8 Å / Axial symmetry: C3
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 181477 / Symmetry type: HELICAL

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