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- PDB-9muf: Cryo-EM structure of the IFI16-PYD filament -

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Basic information

Entry
Database: PDB / ID: 9muf
TitleCryo-EM structure of the IFI16-PYD filament
ComponentsGamma-interferon-inducible protein 16
KeywordsIMMUNE SYSTEM / Innate immune sensor IFI16 / PYD filament / Death domain superfamily / AIM2-like receptors (ALRs) / Cryo-EM structure
Function / homologyHIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / cellular response to interferon-beta / Death-like domain superfamily / activation of innate immune response / Interferon gamma inducible protein 16
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGarg, A. / Niedzialkowska, E. / Egelman, E.H. / Sohn, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)35GM145363 United States
National Science Foundation (NSF, United States)MCB1845003 United States
CitationJournal: EMBO J / Year: 2025
Title: Structural insights into the atypical filament assembly of pyrin domain-containing IFI16.
Authors: Archit Garg / Ewa Niedzialkowska / Jeffrey J Zhou / Jasper Moh / Edward H Egelman / Jungsan Sohn /
Abstract: In response to various intracellular stress or damage-associated signals, inflammasomes can be activated and trigger a pyroptotic cell death process through the sequential assembly of structurally ...In response to various intracellular stress or damage-associated signals, inflammasomes can be activated and trigger a pyroptotic cell death process through the sequential assembly of structurally compatible and interacting filamentous oligomers involving the pyrin domains (PYD) of important inflammasome components. The PYD-containing interferon-inducible protein 16 (IFI16) has been suggested as a viral DNA sensor that can induce inflammasome formation, but it also has other inflammasome-independent functions, including interferon production. Here, the cryo-EM structure of the filament assembled by the PYD of human IFI16 reveals a helical architecture distinct from inflammasome PYD filaments. In silico interface energy calculations suggest that the helical architecture of the IFI16 filament prevents interactions with inflammasome PYD filaments. Biochemical and cell biology experiments consistently demonstrate that IFI16 does not directly interact with inflammasome pyrin domains. Together, our results provide insights into the structural basis of the inflammasome-independent functions of IFI16, and also show that strict architectural compatibility requirements for interactions contribute to the signal transduction specificity in inflammasome signaling.
History
DepositionJan 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-interferon-inducible protein 16
B: Gamma-interferon-inducible protein 16
C: Gamma-interferon-inducible protein 16
D: Gamma-interferon-inducible protein 16
E: Gamma-interferon-inducible protein 16
F: Gamma-interferon-inducible protein 16
G: Gamma-interferon-inducible protein 16
H: Gamma-interferon-inducible protein 16
I: Gamma-interferon-inducible protein 16
J: Gamma-interferon-inducible protein 16
K: Gamma-interferon-inducible protein 16
L: Gamma-interferon-inducible protein 16
M: Gamma-interferon-inducible protein 16
N: Gamma-interferon-inducible protein 16
O: Gamma-interferon-inducible protein 16
P: Gamma-interferon-inducible protein 16
Q: Gamma-interferon-inducible protein 16
R: Gamma-interferon-inducible protein 16


Theoretical massNumber of molelcules
Total (without water)221,46418
Polymers221,46418
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Gamma-interferon-inducible protein 16


Mass: 12303.569 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: Pyrin domain of IFI16 with C-terminal His tag / Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA49X8J6
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filament of Pyrin domain of IFI16 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4cryoSPARC4CTF correction
7UCSF Chimeramodel fitting
9PHENIX1.20.1_4487:model refinement
12cryoSPARC4classification
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 134.6 ° / Axial rise/subunit: 5.6 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148348 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212870
ELECTRON MICROSCOPYf_angle_d0.4517136
ELECTRON MICROSCOPYf_dihedral_angle_d3.3571638
ELECTRON MICROSCOPYf_chiral_restr0.0381980
ELECTRON MICROSCOPYf_plane_restr0.0022106

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