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- EMDB-6845: Flagellin derivative in complex with the NLR protein NAIP5 -

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Basic information

Entry
Database: EMDB / ID: 6845
TitleFlagellin derivative in complex with the NLR protein NAIP5
Map data
SampleFlagellin derivative in complex with NAIP5
  • NAIP5
  • Flagellin
  • Baculoviral IAP repeat-containing protein 1e
  • Phase 2 flagellin,Flagellin
  • ligand
Function / homologyFlagellin, D0/D1 domain / Flagellin D3 domain / Flagellin D3 / NACHT nucleoside triphosphatase / Flagellin / BIR repeat / Leucine-rich repeat domain superfamily / Inhibitor of Apoptosis domain / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region ...Flagellin, D0/D1 domain / Flagellin D3 domain / Flagellin D3 / NACHT nucleoside triphosphatase / Flagellin / BIR repeat / Leucine-rich repeat domain superfamily / Inhibitor of Apoptosis domain / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region / Baculoviral IAP repeat-containing protein 1 / NACHT domain / BIR repeat. / NACHT-NTPase domain profile. / The IPAF inflammasome / MyD88 cascade initiated on plasma membrane / TLR5 cascade / NFkB and MAPK activation mediated by TRAF6 / P-loop containing nucleoside triphosphate hydrolase / BIR repeat profile. / bacterial-type flagellum filament / IPAF inflammasome complex / pyroptosis / positive regulation of interleukin-1 beta production / inhibition of cysteine-type endopeptidase activity involved in apoptotic process / bacterial-type flagellum-dependent cell motility / detection of bacterium / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of canonical Wnt signaling pathway / ubiquitin-protein transferase activity / perikaryon / neuron projection / defense response to Gram-negative bacterium / inflammatory response / neuronal cell body / defense response to bacterium / structural molecule activity / innate immune response / extracellular region / ATP binding / nucleus / metal ion binding / cytoplasm / Flagellin / Phase 2 flagellin / Baculoviral IAP repeat-containing protein 1e / Baculoviral IAP repeat-containing protein 1e
Function and homology information
SourceMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 4.28 Å resolution
AuthorsYang XR / Yang F
CitationJournal: Cell Res. / Year: 2018
Title: Structural basis for specific flagellin recognition by the NLR protein NAIP5.
Authors: Xinru Yang / Fan Yang / Weiguang Wang / Guangzhong Lin / Zehan Hu / Zhifu Han / Yijun Qi / Liman Zhang / Jiawei Wang / Sen-Fang Sui / Jijie Chai
Validation ReportPDB-ID: 5yud

SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2017 / Header (metadata) release: Jan 3, 2018 / Map release: Jan 3, 2018 / Last update: Jan 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0352
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0352
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5yud
  • Surface level: 0.0352
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5yud
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6845.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.31 Å/pix.
= 261.308 Å
200 pix
1.31 Å/pix.
= 261.308 Å
200 pix
1.31 Å/pix.
= 261.308 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density
Contour Level:0.0252 (by author), 0.0352 (movie #1):
Minimum - Maximum-0.08689711 - 0.23340823
Average (Standard dev.)6.1092534E-5 (0.0076064058)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0870.2330.000

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Supplemental data

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Sample components

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Entire Flagellin derivative in complex with NAIP5

EntireName: Flagellin derivative in complex with NAIP5 / Number of components: 6

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Component #1: protein, Flagellin derivative in complex with NAIP5

ProteinName: Flagellin derivative in complex with NAIP5 / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, NAIP5

ProteinName: NAIP5 / Recombinant expression: No

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Component #3: protein, Flagellin

ProteinName: Flagellin / Recombinant expression: No

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Component #4: protein, Baculoviral IAP repeat-containing protein 1e

ProteinName: Baculoviral IAP repeat-containing protein 1e / Recombinant expression: No
MassTheoretical: 160.018047 kDa
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #5: protein, Phase 2 flagellin,Flagellin

ProteinName: Phase 2 flagellin,Flagellin / Recombinant expression: No
MassTheoretical: 7.665362 kDa
Source (engineered)Expression System: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720

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Component #6: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 626608
3D reconstructionResolution: 4.28 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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