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- PDB-5yud: Flagellin derivative in complex with the NLR protein NAIP5 -

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Basic information

Entry
Database: PDB / ID: 5yud
TitleFlagellin derivative in complex with the NLR protein NAIP5
Components
  • Baculoviral IAP repeat-containing protein 1e
  • Phase 2 flagellin,Flagellin
KeywordsIMMUNE SYSTEM / Flagellin / NAIP5 / NLRC4 / Cryo-EM
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 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / pyroptotic inflammatory response / 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 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / pyroptotic inflammatory response / detection of bacterium / positive regulation of interleukin-1 beta production / defense response to Gram-negative bacterium / defense response to bacterium / receptor ligand activity / inflammatory response / innate immune response / apoptotic process / symbiont entry into host cell / negative regulation of 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 / NOD2 winged helix domain / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / BIR repeat. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / 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
ADENOSINE-5'-TRIPHOSPHATE / 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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsYang, X.R. / Yang, F. / Wang, W.G. / Lin, G.Z.
Funding support China, 6items
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, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 3, 2018Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 1e
C: Phase 2 flagellin,Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,1913
Polymers167,6832
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-39 kcal/mol
Surface area63030 Å2

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Components

#1: Protein Baculoviral IAP repeat-containing protein 1e / NLR family / apoptosis inhibitory protein 5 / Neuronal apoptosis inhibitory protein 5


Mass: 160018.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Naip5, Birc1e / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8CGT2, UniProt: Q9R016*PLUS
#2: Protein Phase 2 flagellin,Flagellin / Phase 1-I flagellin


Mass: 7665.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fljB, H2, STM2771, fliC, flaF, hag, STM1959 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P52616, UniProt: P06179
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Flagellin derivative in complex with NAIP5COMPLEX#1-#20RECOMBINANT
2NAIP5COMPLEX#11RECOMBINANT
3FlagellinCOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Mus musculus (house mouse)10090
31Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)99287LT2 / SGSC1412 / ATCC 700720
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Spodoptera frugiperda (fall armyworm)7108
31Escherichia coli K-12 (bacteria)83333K-12
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626608 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00810675
ELECTRON MICROSCOPYf_angle_d1.17514446
ELECTRON MICROSCOPYf_dihedral_angle_d8.9128895
ELECTRON MICROSCOPYf_chiral_restr0.0561627
ELECTRON MICROSCOPYf_plane_restr0.0061857

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