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- EMDB-48631: Cryo-EM structure of the IFI16-PYD filament -

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Basic information

Entry
Database: EMDB / ID: EMD-48631
TitleCryo-EM structure of the IFI16-PYD filament
Map dataCryo-EM structure of the IFI16-PYD filament reveals a helical architecture distinct from inflammasome PYD filaments
Sample
  • Complex: Filament of Pyrin domain of IFI16
    • Protein or peptide: Gamma-interferon-inducible protein 16
KeywordsInnate immune sensor IFI16 / PYD filament / Death domain superfamily / AIM2-like receptors (ALRs) / Cryo-EM structure / IMMUNE SYSTEM
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGarg A / Niedzialkowska E / Egelman EH / Sohn J
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48631.png

Downloads & links

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Map

FileDownload / File: emd_48631.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the IFI16-PYD filament reveals a helical architecture distinct from inflammasome PYD filaments
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 256 pix.
= 298.24 Å		1.17 Å/pix.
x 256 pix.
= 298.24 Å		1.17 Å/pix.
x 256 pix.
= 298.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.165 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.6632708 - 1.1795275
Average (Standard dev.)0.00087547576 (±0.04277047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 298.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48631_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_48631_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 : Filament of Pyrin domain of IFI16

EntireName: Filament of Pyrin domain of IFI16
Components
  • Complex: Filament of Pyrin domain of IFI16
    • Protein or peptide: Gamma-interferon-inducible protein 16

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Supramolecule #1: Filament of Pyrin domain of IFI16

SupramoleculeName: Filament of Pyrin domain of IFI16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gamma-interferon-inducible protein 16

MacromoleculeName: Gamma-interferon-inducible protein 16 / type: protein_or_peptide / ID: 1 / Details: Pyrin domain of IFI16 with C-terminal His tag / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.303569 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSVKMGKKYK NIVLLKGLEV INDYHFRMVK SLLSNDLKLN LKMREEYDKI QIADLMEEKF RGDAGLGKLI KIFEDIPTLE DLAETLKKE KLKVKGPALE HHHHHH

UniProtKB: Interferon gamma inducible protein 16

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 120000

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 134.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 148348
CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

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

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