[English] 日本語
![](img/lk-miru.gif)
- PDB-8fml: Cryo-EM structure of NLR family apoptosis inhibitory protein 5 (N... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8fml | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of NLR family apoptosis inhibitory protein 5 (NAIP5) in complex with a full-length flagellin (FliC) ligand | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / Inflammasome / Innate immunity / Bacterial ligand / host-pathogen interaction / Protein complex | ||||||
Function / homology | ![]() TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / IPAF inflammasome complex / bacterial-type flagellum / pyroptotic inflammatory response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / detection of bacterium / positive regulation of interleukin-1 beta production ...TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / The IPAF inflammasome / IPAF inflammasome complex / bacterial-type flagellum / pyroptotic inflammatory response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / detection of bacterium / positive regulation of interleukin-1 beta production / perikaryon / defense response to Gram-negative bacterium / defense response to bacterium / symbiont entry into host cell / inflammatory response / innate immune response / neuronal cell body / apoptotic process / negative regulation of apoptotic process / structural molecule activity / extracellular region / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
![]() | Paidimuddala, B. / Zhang, L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for flagellin-induced NAIP5 activation. Authors: Bhaskar Paidimuddala / Jianhao Cao / Liman Zhang / ![]() Abstract: The NAIP (NLR family apoptosis inhibitory protein)/NLRC4 (NLR family CARD containing protein 4) inflammasome senses Gram-negative bacterial ligand. In the ligand-bound state, the winged helix domain ...The NAIP (NLR family apoptosis inhibitory protein)/NLRC4 (NLR family CARD containing protein 4) inflammasome senses Gram-negative bacterial ligand. In the ligand-bound state, the winged helix domain of NAIP forms a steric clash with NLRC4 to open it up. However, how ligand binding activates NAIP is less clear. Here, we investigated the dynamics of the ligand-binding region of inactive NAIP5 and solved the cryo-EM structure of NAIP5 in complex with its specific ligand, FliC from flagellin, at 2.9-Å resolution. The structure revealed a "trap and lock" mechanism in FliC recognition, whereby FliC-D0 is first trapped by the hydrophobic pocket of NAIP5, then locked in the binding site by ID (insertion domain) and C-terminal tail of NAIP5. The FliC-D0 domain further inserts into ID to stabilize the complex. According to this mechanism, FliC triggers the conformational change of NAIP5 by bringing multiple flexible domains together. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 305.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 235.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 69.9 KB | Display | |
Data in CIF | ![]() | 100.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 29296MC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 161128.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 52614.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: fliC, flaF, hag, STM1959 / Plasmid: pCMV-His-fliC / Cell line (production host): HEK293 / Production host: ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: NAIP5 in complex with a full-length bacterial flagellin ligand (FliC) Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 0.2135 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4616 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 199022 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL | ||||||||||||||||||||||||||||
Refine LS restraints |
|