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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: EMD-6845
TitleFlagellin derivative in complex with the NLR protein NAIP5
Map data
Sample
  • Complex: Flagellin derivative in complex with NAIP5
    • Complex: NAIP5
      • Protein or peptide: Baculoviral IAP repeat-containing protein 1e
    • Complex: Flagellin
      • Protein or peptide: Phase 2 flagellin,Flagellin
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsFlagellin / NAIP5 / NLRC4 / Cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / IPAF inflammasome complex / The IPAF inflammasome / 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 / IPAF inflammasome complex / The IPAF inflammasome / 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 / receptor ligand activity / defense response to bacterium / inflammatory response / symbiont entry into host cell / innate immune response / neuronal cell body / negative regulation of apoptotic process / apoptotic process / structural molecule activity / extracellular space / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Baculoviral IAP repeat-containing protein 1 / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / Flagellin, C-terminal domain, subdomain 2 ...Baculoviral IAP repeat-containing protein 1 / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / NLRC4, helical domain / : / NLRC4 helical domain / Nlrc4-like, winged helix domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Flagellin / Phase 2 flagellin / Baculoviral IAP repeat-containing protein 1e / Baculoviral IAP repeat-containing protein 1e
Similarity search - Component
Biological speciesMus musculus (house mouse) / Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsYang XR / Yang F
Funding support China, 6 items
OrganizationGrant numberCountry
Chinese Ministry of Science and Techonolgy2014CB910101 China
Chinese Ministry of Science and Techonolgy2016YFA0501101 China
Chinese Ministry of Science and Techonolgy2017YFA0504600 China
National Natural Science Foundation of China31230016 China
National Natural Science Foundation of China31370717 China
National Natural Science Foundation of China31670745 China
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 /
Abstract: The nucleotide-binding domain- and leucine-rich repeat (LRR)-containing proteins (NLRs) function as intracellular immune receptors to detect the presence of pathogen- or host-derived signals. The ...The nucleotide-binding domain- and leucine-rich repeat (LRR)-containing proteins (NLRs) function as intracellular immune receptors to detect the presence of pathogen- or host-derived signals. The mechanisms of how NLRs sense their ligands remain elusive. Here we report the structure of a bacterial flagellin derivative in complex with the NLR proteins NAIP5 and NLRC4 determined by cryo-electron microscopy at 4.28 Å resolution. The structure revealed that the flagellin derivative forms two parallel helices interacting with multiple domains including BIR1 and LRR of NAIP5. Binding to NAIP5 results in a nearly complete burial of the flagellin derivative, thus stabilizing the active conformation of NAIP5. The extreme C-terminal side of the flagellin is anchored to a sterically constrained binding pocket of NAIP5, which likely acts as a structural determinant for discrimination of different bacterial flagellins by NAIP5, a notion further supported by biochemical data. Taken together, our results shed light on the molecular mechanisms underlying NLR ligand perception.
History
DepositionNov 21, 2017-
Header (metadata) releaseJan 3, 2018-
Map releaseJan 3, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

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

emd_6845.png

Downloads & links

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Map

FileDownload / File: emd_6845.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0252 / Movie #1: 0.0352
Minimum - Maximum-0.08689711 - 0.23340823
Average (Standard dev.)0.000061092534 (±0.0076064058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: Flagellin derivative in complex with NAIP5
    • Complex: NAIP5
      • Protein or peptide: Baculoviral IAP repeat-containing protein 1e
    • Complex: Flagellin
      • Protein or peptide: Phase 2 flagellin,Flagellin
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Flagellin derivative in complex with NAIP5

SupramoleculeName: Flagellin derivative in complex with NAIP5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: NAIP5

SupramoleculeName: NAIP5 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: Flagellin

SupramoleculeName: Flagellin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: Baculoviral IAP repeat-containing protein 1e

MacromoleculeName: Baculoviral IAP repeat-containing protein 1e / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 160.018047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEHGESSED RISEIDYEFL PELSALLGVD AFQVAKSQEE EEHKERMKMK KGFNSQMRSE AKRLKTFETY DTFRSWTPQE MAAAGFYHT GVRLGVQCFC CSLILFGNSL RKLPIERHKK LRPECEFLQG KDVGNIGKYD IRVKRPEKML RGGKARYHEE E ARLESFED ...String:
MAEHGESSED RISEIDYEFL PELSALLGVD AFQVAKSQEE EEHKERMKMK KGFNSQMRSE AKRLKTFETY DTFRSWTPQE MAAAGFYHT GVRLGVQCFC CSLILFGNSL RKLPIERHKK LRPECEFLQG KDVGNIGKYD IRVKRPEKML RGGKARYHEE E ARLESFED WPFYAHGTSP RVLSAAGFVF TGKRDTVQCF SCGGSLGNWE EGDDPWKEHA KWFPKCEFLQ SKKSSEEIAQ YI QSYEGFV HVTGEHFVKS WVRRELPMVS AYCNDSVFAN EELRMDMFKD WPQESPVGVE ALVRAGFFYT GKKDIVRCFS CGG CLEKWA EGDDPMEDHI KFFPECVFLQ TLKSSAEVIP TLQSQYALPE ATETTRESNH GDAAAVHSTV VDLGRSEAQW FQEA RSLSE QLRDNYTKAT FRHMNLPEVC SSLGTDHLLS CDVSIISKHI SQPVQEALTI PEVFSNLNSV MCVEGETGSG KTTFL KRIA FLWASGCCPL LYRFQLVFYL SLSSITPDQG LANIICAQLL GAGGCISEVC LSSSIQQLQH QVLFLLDDYS GLASLP QAL HTLITKNYLS RTCLLIAVHT NRVRDIRLYL GTSLEIQEFP FYNTVSVLRK FFSHDIICVE KLIIYFIDNK DLQGVYK TP LFVAAVCTDW IQNASAQDKF QDVTLFQSYM QYLSLKYKAT AEPLQATVSS CGQLALTGLF SSCFEFNSDD LAEAGVDE D EKLTTLLMSK FTAQRLRPVY RFLGPLFQEF LAAVRLTELL SSDRQEDQDL GLYYLRQIDS PLKAINSFNI FLYYVSSHS SSKAAPTVVS HLLQLVDEKE SLENMSENED YMKLHPQTFL WFQFVRGLWL VSPESSSSFV SEHLLRLALI FAYESNTVAE CSPFILQFL RGKTLALRVL NLQYFRDHPE SLLLLRSLKV SINGNKMSSY VDYSFKTYFE NLQPPAIDEE YTSAFEHISE W RRNFAQDE EIIKNYENIR PRALPDISEG YWKLSPKPCK IPKLEVQVNN TDAADQALLQ VLMEVFSASQ SIEFRLFNSS GF LESICPA LELSKASVTK CSMSRLELSR AEQELLLTLP ALQSLEVSET NQLPEQLFHN LHKFLGLKEL CVRLDGKPNV LSV LPREFP NLLHMEKLSI QTSTESDLSK LVKFIQNFPN LHVFHLKCDF LSNCESLMAV LASCKKLREI EFSGRCFEAM TFVN ILPNF VSLKILNLKD QQFPDKETSE KFAQALGSLR NLEELLVPTG DGIHQVAKLI VRQCLQLPCL RVLTFHDILD DDSVI EIAR AATSGGFQKL ENLDISMNHK ITEEGYRNFF QALDNLPNLQ ELNICRNIPG RIQVQATTVK ALGQCVSRLP SLIRLH MLS WLLDEEDMKV INDVKERHPQ SKRLIIFWKL IVPFSPVILE

UniProtKB: Baculoviral IAP repeat-containing protein 1e

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Macromolecule #2: Phase 2 flagellin,Flagellin

MacromoleculeName: Phase 2 flagellin,Flagellin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720
Molecular weightTheoretical: 7.665362 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
AAARLSSGLR INSAKDDAAG QAIANSGSGS GSRIEDSDYA TEVSNMSRAQ ILQQAGTSVL AQANQVPQNV LSLLR

UniProtKB: Phase 2 flagellin, Flagellin

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626608
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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