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- EMDB-63154: Human IFI16 PYD filament structure -

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Basic information

Entry
Database: EMDB / ID: EMD-63154
TitleHuman IFI16 PYD filament structure
Map data
Sample
  • Complex: Human IFI16 PYD filament
    • Protein or peptide: Gamma-interferon-inducible protein 16
KeywordsPYD / filament / pyrin / IFI16 / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / negative regulation of gene expression, epigenetic / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / monocyte differentiation ...negative regulation of AIM2 inflammasome complex assembly / negative regulation of DNA binding / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of viral genome replication / negative regulation of gene expression, epigenetic / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / monocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to glucose starvation / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / cellular response to ionizing radiation / autophagy / regulation of inflammatory response / double-stranded DNA binding / defense response to virus / nuclear speck / regulation of autophagy / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsTakahashi R / Zhang Z / Ohto U / Shimizu T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human IFI16 PYD filament structure
Authors: Takahashi R
History
DepositionJan 15, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63154.png

Downloads & links

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Map

FileDownload / File: emd_63154.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 160 pix.
= 212.48 Å		1.33 Å/pix.
x 160 pix.
= 212.48 Å		1.33 Å/pix.
x 160 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.3063812 - 2.2582746
Average (Standard dev.)0.006440876 (±0.11086778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_63154_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63154_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63154_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 : Human IFI16 PYD filament

EntireName: Human IFI16 PYD filament
Components
  • Complex: Human IFI16 PYD filament
    • Protein or peptide: Gamma-interferon-inducible protein 16

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Supramolecule #1: Human IFI16 PYD filament

SupramoleculeName: Human IFI16 PYD filament / 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 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.429393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GKKYKNIVLL KGLEVINDYH FRMVKSLLSN DLKLNLKMRE EYDKIQIADL MEEKFRGDAG LGKLIKIFED IPTLEDLAET LKKEKLKVK

UniProtKB: Gamma-interferon-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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 134.553 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 183411
CTF correctionType: NONE
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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