[English] 日本語
Yorodumi
- PDB-8fvu: Cryo-EM structure of human Needle/NAIP/NLRC4 (R288A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fvu
TitleCryo-EM structure of human Needle/NAIP/NLRC4 (R288A)
Components
  • Baculoviral IAP repeat-containing protein 1
  • Lethal factor,Type III secretion system proteinType three secretion system
  • NLR family CARD domain-containing protein 4
KeywordsIMMUNE SYSTEM / NLRC4 / NAIP / Inflammasome
Function / homology
Function and homology information


anthrax lethal factor endopeptidase / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / type III protein secretion system complex / caspase binding / positive regulation of protein processing / protein secretion by the type III secretion system / protein serine/threonine kinase binding ...anthrax lethal factor endopeptidase / IPAF inflammasome complex / The IPAF inflammasome / icosanoid biosynthetic process / canonical inflammasome complex / type III protein secretion system complex / caspase binding / positive regulation of protein processing / protein secretion by the type III secretion system / protein serine/threonine kinase binding / activation of cysteine-type endopeptidase activity / host cell cytosol / pattern recognition receptor signaling pathway / cysteine-type endopeptidase inhibitor activity / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Uptake and function of anthrax toxins / endopeptidase activator activity / negative regulation of tumor necrosis factor-mediated signaling pathway / detection of bacterium / activation of innate immune response / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / protein homooligomerization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / metalloendopeptidase activity / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / metallopeptidase activity / nervous system development / positive regulation of NF-kappaB transcription factor activity / toxin activity / basolateral plasma membrane / regulation of apoptotic process / negative regulation of neuron apoptotic process / defense response to bacterium / inflammatory response / positive regulation of apoptotic process / innate immune response / intracellular membrane-bounded organelle / apoptotic process / negative regulation of apoptotic process / magnesium ion binding / cell surface / ATP hydrolysis activity / protein homodimerization activity / proteolysis / zinc ion binding / extracellular region / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Baculoviral IAP repeat-containing protein 1 / NLR family CARD domain-containing protein 4 / NLRC4, helical domain / NLRC4 helical domain / Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein ...Baculoviral IAP repeat-containing protein 1 / NLR family CARD domain-containing protein 4 / NLRC4, helical domain / NLRC4 helical domain / Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Type III secretion, needle-protein-like / Type III secretion, needle-protein-like superfamily / Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF / Type III secretion system, needle protein / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / 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 / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Metallopeptidase, catalytic domain superfamily / Death-like domain superfamily / Leucine-rich repeat domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Lethal factor / Baculoviral IAP repeat-containing protein 1 / Type III secretion system protein / NLR family CARD domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus anthracis (anthrax bacterium)
Burkholderia (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMatico, R.E. / Yu, X. / Miller, R. / Somani, S. / Ricketts, M.D. / Kumar, N. / Steele, R.A. / Medley, Q. / Berger, S. / Faustin, B. / Sharma, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of the human NAIP/NLRC4 inflammasome assembly and pathogen sensing.
Authors: Rosalie E Matico / Xiaodi Yu / Robyn Miller / Sandeep Somani / M Daniel Ricketts / Nikit Kumar / Ruth A Steele / Quintus Medley / Scott Berger / Benjamin Faustin / Sujata Sharma /
Abstract: The NLR family caspase activation and recruitment domain-containing 4 (NLRC4) inflammasome is a critical cytosolic innate immune machine formed upon the direct sensing of bacterial infection and in ...The NLR family caspase activation and recruitment domain-containing 4 (NLRC4) inflammasome is a critical cytosolic innate immune machine formed upon the direct sensing of bacterial infection and in response to cell stress during sterile chronic inflammation. Despite its major role in instigating the subsequent host immune response, a more complete understanding of the molecular events in the formation of the NLRC4 inflammasome in humans is lacking. Here we identify Bacillus thailandensis type III secretion system needle protein (Needle) as a potent trigger of the human NLR family apoptosis inhibitory protein (NAIP)/NLRC4 inflammasome complex formation and determine its structural features by cryogenic electron microscopy. We also provide a detailed understanding of how type III secretion system pathogen components are sensed by human NAIP to form a cascade of NLRC4 protomer through a critical lasso-like motif, a 'lock-key' activation model and large structural rearrangement, ultimately forming the full human NLRC4 inflammasome. These results shed light on key regulatory mechanisms specific to the NLRC4 inflammasome assembly, and the innate immune modalities of pathogen sensing in humans.
History
DepositionJan 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 1
B: NLR family CARD domain-containing protein 4
U: Lethal factor,Type III secretion system protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,9607
Polymers320,2573
Non-polymers7034
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Baculoviral IAP repeat-containing protein 1 / Neuronal apoptosis inhibitory protein


Mass: 160484.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAIP, BIRC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13075
#2: Protein NLR family CARD domain-containing protein 4 / CARD / LRR / and NACHT-containing protein / CED-4-like protein Clan / Caspase recruitment domain- ...CARD / LRR / and NACHT-containing protein / CED-4-like protein Clan / Caspase recruitment domain-containing protein 12 / Ice protease-activating factor / Ipaf


Mass: 116941.531 Da / Num. of mol.: 1 / Mutation: R288A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLRC4, CARD12, CLAN, CLAN1, IPAF, UNQ6189/PRO20215 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPP4
#3: Protein Lethal factor,Type III secretion system protein / Type three secretion system / LF / Anthrax lethal toxin endopeptidase component


Mass: 42830.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium), (gene. exp.) Burkholderia (bacteria)
Gene: lef, pXO1-107, BXA0172, GBAA_pXO1_0172, BPSS1548 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P15917, UniProt: Q63K18, anthrax lethal factor endopeptidase
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1the complex of Needle, human NAIP and NLRC4COMPLEX#1-#30MULTIPLE SOURCES
2human NAIP and NLRC4COMPLEX#1-#21RECOMBINANT
3Burkholderia Needle (chimeric with an anthrax toxin lethal factor tag)COMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Bacillus anthracis (anthrax bacterium)1392
43Burkholderia (bacteria)32008
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106381 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more