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- EMDB-29296: Cryo-EM structure of NLR family apoptosis inhibitory protein 5 (N... -

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Basic information

Entry
Database: EMDB / ID: EMD-29296
TitleCryo-EM structure of NLR family apoptosis inhibitory protein 5 (NAIP5) in complex with a full-length flagellin (FliC) ligand
Map data
Sample
  • Complex: NAIP5 in complex with a full-length bacterial flagellin ligand (FliC)
    • Protein or peptide: Baculoviral IAP repeat-containing protein 1e
    • Protein or peptide: Flagellin
KeywordsInflammasome / Innate immunity / Bacterial ligand / host-pathogen interaction / Protein complex / IMMUNE SYSTEM
Function / homology
Function and homology information


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
: / Flagellin, barrel domain / Baculoviral IAP repeat-containing protein 1 / Flagellin D3 / Flagellin D3 domain / NLRC4, helical domain / NLRC4 helical domain / Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region ...: / Flagellin, barrel domain / Baculoviral IAP repeat-containing protein 1 / Flagellin D3 / Flagellin D3 domain / NLRC4, helical domain / NLRC4 helical 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 / NOD2, winged helix domain / NOD2 winged helix domain / 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 / Baculoviral IAP repeat-containing protein 1e
Similarity search - Component
Biological speciesMus musculus (house mouse) / Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsPaidimuddala B / Zhang L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2023
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
DepositionDec 23, 2022-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29296.png

Downloads & links

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Map

FileDownload / File: emd_29296.map.gz / Format: CCP4 / Size: 944.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.528 Å
Density
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.023458567 - 2.514411
Average (Standard dev.)0.00078196387 (±0.01939407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions628628628
Spacing628628628
CellA=B=C: 331.58398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29296_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29296_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NAIP5 in complex with a full-length bacterial flagellin ligand (FliC)

EntireName: NAIP5 in complex with a full-length bacterial flagellin ligand (FliC)
Components
  • Complex: NAIP5 in complex with a full-length bacterial flagellin ligand (FliC)
    • Protein or peptide: Baculoviral IAP repeat-containing protein 1e
    • Protein or peptide: Flagellin

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Supramolecule #1: NAIP5 in complex with a full-length bacterial flagellin ligand (FliC)

SupramoleculeName: NAIP5 in complex with a full-length bacterial flagellin ligand (FliC)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 213.5 KDa

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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: 161.128156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKL AEHGESSEDR ISEIDYEFLP ELSALLGVDA FQVAKSQEEE EHKERMKMKK GFNSQMRSEA KRLKTFETYD TFRSWTPQE MAAAGFYHTG VRLGVQCFCC SLILFGNSLR KLPIERHKKL RPECEFLQGK DVGNIGKYDI RVKRPEKMLR G GKARYHEE ...String:
MDYKDDDDKL AEHGESSEDR ISEIDYEFLP ELSALLGVDA FQVAKSQEEE EHKERMKMKK GFNSQMRSEA KRLKTFETYD TFRSWTPQE MAAAGFYHTG VRLGVQCFCC SLILFGNSLR KLPIERHKKL RPECEFLQGK DVGNIGKYDI RVKRPEKMLR G GKARYHEE EARLESFEDW PFYAHGTSPR VLSAAGFVFT GKRDTVQCFS CGGSLGNWEE GDDPWKEHAK WFPKCEFLQS KK SSEEIAQ YIQSYEGFVH VTGEHFVKSW VRRELPMVSA YCNDSVFANE ELRMDMFKDW PQESPVGVEA LVRAGFFYTG KKD IVRCFS CGGCLEKWAE GDDPMEDHIK FFPECVFLQT LKSSAEVIPT LQSQYALPEA TETTRESNHG DAAAVHSTVV DLGR SEAQW FQEARSLSEQ LRDNYTKATF RHMNLPEVCS SLGTDHLLSC DVSIISKHIS QPVQEALTIP EVFSNLNSVM CVEGE TGSG KTTFLKRIAF LWASGCCPLL YRFQLVFYLS LSSITPDQGL ANIICAQLLG AGGCISEVCL SSSIQQLQHQ VLFLLD DYS GLASLPQALH TLITKNYLSR TCLLIAVHTN RVRDIRLYLG TSLEIQEFPF YNTVSVLRKF FSHDIICVEK LIIYFID NK DLQGVYKTPL FVAAVCTDWI QNASAQDKFQ DVTLFQSYMQ YLSLKYKATA EPLQATVSSC GQLALTGLFS SCFEFNSD D LAEAGVDEDE KLTTLLMSKF TAQRLRPVYR FLGPLFQEFL AAVRLTELLS SDRQEDQDLG LYYLRQIDSP LKAINSFNI FLYYVSSHSS SKAAPTVVSH LLQLVDEKES LENMSENEDY MKLHPQTFLW FQFVRGLWLV SPESSSSFVS EHLLRLALIF AYESNTVAE CSPFILQFLR GKTLALRVLN LQYFRDHPES LLLLRSLKVS INGNKMSSYV DYSFKTYFEN LQPPAIDEEY T SAFEHISE WRRNFAQDEE IIKNYENIRP RALPDISEGY WKLSPKPCKI PKLEVQVNNT DAADQALLQV LMEVFSASQS IE FRLFNSS GFLESICPAL ELSKASVTKC SMSRLELSRA EQELLLTLPA LQSLEVSETN QLPEQLFHNL HKFLGLKELC VRL DGKPNV LSVLPREFPN LLHMEKLSIQ TSTESDLSKL VKFIQNFPNL HVFHLKCDFL SNCESLMAVL ASCKKLREIE FSGR CFEAM TFVNILPNFV SLKILNLKDQ QFPDKETSEK FAQALGSLRN LEELLVPTGD GIHQVAKLIV RQCLQLPCLR VLTFH DILD DDSVIEIARA ATSGGFQKLE NLDISMNHKI TEEGYRNFFQ ALDNLPNLQE LNICRNIPGR IQVQATTVKA LGQCVS RLP SLIRLHMLSW LLDEEDMKVI NDVKERHPQS KRLIIFWKLI VPFSPVILE

UniProtKB: Baculoviral IAP repeat-containing protein 1e

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Macromolecule #2: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Molecular weightTheoretical: 52.614418 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHMAQ VINTNSLSLL TQNNLNKSQS ALGTAIERLS SGLRINSAKD DAAGQAIANR FTANIKGLTQ ASRNANDGIS IAQTTEGAL NEINNNLQRV RELAVQSANS TNSQSDLDSI QAEITQRLNE IDRVSGQTQF NGVKVLAQDN TLTIQVGAND G ETIDIDLK ...String:
MHHHHHHMAQ VINTNSLSLL TQNNLNKSQS ALGTAIERLS SGLRINSAKD DAAGQAIANR FTANIKGLTQ ASRNANDGIS IAQTTEGAL NEINNNLQRV RELAVQSANS TNSQSDLDSI QAEITQRLNE IDRVSGQTQF NGVKVLAQDN TLTIQVGAND G ETIDIDLK QINSQTLGLD TLNVQQKYKV SDTAATVTGY ADTTIALDNS TFKASATGLG GTDQKIDGDL KFDDTTGKYY AK VTVTGGT GKDGYYEVSV DKTNGEVTLA GGATSPLTGG LPATATEDVK NVQVANADLT EAKAALTAAG VTGTASVVKM SYT DNNGKT IDGGLAVKVG DDYYSATQNK DGSISINTTK YTADDGTSKT ALNKLGGADG KTEVVSIGGK TYAASKAEGH NFKA QPDLA EAAATTTENP LQKIDAALAQ VDTLRSDLGA VQNRFNSAIT NLGNTVNNLT SARSRIEDSD YATEVSNMSR AQILQ QAGT SVLAQANQVP QNVLSLLR

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4616 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5yud

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 199022
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-8fml:
Cryo-EM structure of NLR family apoptosis inhibitory protein 5 (NAIP5) in complex with a full-length flagellin (FliC) ligand

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