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- PDB-6n1i: Cryo-EM structure of NLRC4-CARD filament -

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Basic information

Entry
Database: PDB / ID: 6n1i
TitleCryo-EM structure of NLRC4-CARD filament
ComponentsNLR family CARD domain-containing protein 4
KeywordsSIGNALING PROTEIN / Inflammasome / filament / immunity
Function / homologyCaspase recruitment domain / Death-like domain superfamily / NACHT nucleoside triphosphatase / NACHT domain / CARD caspase recruitment domain profile. / CARD domain / NACHT-NTPase domain profile. / P-loop containing nucleoside triphosphate hydrolase / Leucine-rich repeat domain superfamily / TP53 Regulates Transcription of Caspase Activators and Caspases ...Caspase recruitment domain / Death-like domain superfamily / NACHT nucleoside triphosphatase / NACHT domain / CARD caspase recruitment domain profile. / CARD domain / NACHT-NTPase domain profile. / P-loop containing nucleoside triphosphate hydrolase / Leucine-rich repeat domain superfamily / TP53 Regulates Transcription of Caspase Activators and Caspases / The IPAF inflammasome / pyroptosis / interleukin-1 beta secretion / IPAF inflammasome complex / detection of bacterium / activation of innate immune response / activation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of apoptotic process / protein homooligomerization / positive regulation of NF-kappaB transcription factor activity / inflammatory response / positive regulation of apoptotic process / defense response to bacterium / apoptotic process / innate immune response / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / NLR family CARD domain-containing protein 4
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.58 Å resolution
AuthorsLi, Y. / Fu, T. / Wu, H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Cryo-EM structures of ASC and NLRC4 CARD filaments reveal a unified mechanism of nucleation and activation of caspase-1.
Authors: Yang Li / Tian-Min Fu / Alvin Lu / Kristen Witt / Jianbin Ruan / Chen Shen / Hao Wu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 8, 2018 / Release: Dec 5, 2018

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Assembly

Deposited unit
A: NLR family CARD domain-containing protein 4
B: NLR family CARD domain-containing protein 4
C: NLR family CARD domain-containing protein 4
D: NLR family CARD domain-containing protein 4
E: NLR family CARD domain-containing protein 4
F: NLR family CARD domain-containing protein 4
G: NLR family CARD domain-containing protein 4
H: NLR family CARD domain-containing protein 4
I: NLR family CARD domain-containing protein 4
J: NLR family CARD domain-containing protein 4
K: NLR family CARD domain-containing protein 4
L: NLR family CARD domain-containing protein 4
M: NLR family CARD domain-containing protein 4
N: NLR family CARD domain-containing protein 4
O: NLR family CARD domain-containing protein 4
P: NLR family CARD domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)159,80316
Polyers159,80316
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)31960
ΔGint (kcal/M)-54
Surface area (Å2)51290
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 16 / Rise per n subunits: 4.93 Å / Rotation per n subunits: -100.48 deg.

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Components

#1: Protein/peptide
NLR family CARD domain-containing protein 4 / CARD / LRR / and NACHT-containing protein / Clan protein / Caspase recruitment domain-containing protein 12 / Ice protease-activating factor / Ipaf


Mass: 9987.671 Da / Num. of mol.: 16 / Fragment: CARD (UNP residues 1-85) / Source: (gene. exp.) Homo sapiens (human) / Gene: NLRC4, CARD12, CLAN, CLAN1, IPAF, UNQ6189/PRO20215 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPP4

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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: NLRC4-CARD filament / Type: CELL / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding 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: 41 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -100.48 deg. / Axial rise/subunit: 4.93 Å / Axial symmetry: C1
3D reconstructionResolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 199312 / Symmetry type: HELICAL

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