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- PDB-9lji: Human IFI16 PYD filament structure -

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Basic information

Entry
Database: PDB / ID: 9lji
TitleHuman IFI16 PYD filament structure
ComponentsGamma-interferon-inducible protein 16
KeywordsIMMUNE SYSTEM / PYD / filament / pyrin / IFI16
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsTakahashi, R. / Zhang, Z. / Ohto, U. / Shimizu, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human IFI16 PYD filament structure
Authors: Takahashi, R.
History
DepositionJan 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: Gamma-interferon-inducible protein 16
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
S: Gamma-interferon-inducible protein 16
T: Gamma-interferon-inducible protein 16
U: Gamma-interferon-inducible protein 16


Theoretical massNumber of molelcules
Total (without water)219,01721
Polymers219,01721
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 / Ifi-16 / Interferon-inducible myeloid differentiation transcriptional activator


Mass: 10429.393 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16666
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: Human IFI16 PYD filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 134.553 ° / Axial rise/subunit: 5.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183411 / Symmetry type: HELICAL
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00115204
ELECTRON MICROSCOPYf_angle_d0.30420223
ELECTRON MICROSCOPYf_dihedral_angle_d2.411932
ELECTRON MICROSCOPYf_chiral_restr0.0352331
ELECTRON MICROSCOPYf_plane_restr0.0012478

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