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- PDB-9r0s: human FAM118B pentameric filament -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9r0s
Titlehuman FAM118B pentameric filament
ComponentsProtein FAM118B
KeywordsIMMUNE SYSTEM / filament / enzyme / NAD / nucleus / innate immunity / sirtuin
Function / homologyProtein FAM118 / SIR2-like domain / Cajal body / identical protein binding / Protein FAM118B
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsBaretic, D. / Missoury, S. / Patel, K. / Coste, F. / Delarue, M. / Suskiewicz, J.M. / Ahel, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Filament formation and NAD processing by noncanonical human FAM118 sirtuins.
Authors: Domagoj Baretić / Sophia Missoury / Karishma Patel / Maximilien Martinez / Franck Coste / Kang Zhu / Rebecca Smith / Anna Georgina Kopasz / Yang Lu / Nicolas Bigot / Catherine Chapuis / ...Authors: Domagoj Baretić / Sophia Missoury / Karishma Patel / Maximilien Martinez / Franck Coste / Kang Zhu / Rebecca Smith / Anna Georgina Kopasz / Yang Lu / Nicolas Bigot / Catherine Chapuis / Romane Riou / Nina Đukić / Stéphane Goffinont / Valentin Pressoir / Sara Patačko / Gyula Timinszky / Marc Delarue / Bertrand Castaing / Dragana Ahel / Andreja Mikoč / Sébastien Huet / Ivan Ahel / Marcin J Suskiewicz /
Abstract: Sirtuins are an ancient family of enzymes with diverse nicotinamide adenine dinucleotide (NAD)-dependent activities. Here we identify family with sequence similarity 118 member B (FAM118B) and ...Sirtuins are an ancient family of enzymes with diverse nicotinamide adenine dinucleotide (NAD)-dependent activities. Here we identify family with sequence similarity 118 member B (FAM118B) and FAM118A-two understudied vertebrate proteins-as vertebrate-specific sirtuins with similarities to bacterial antiphage sirtuins. We show that human FAM118B forms head-to-tail filaments both in vitro and in living human cells, a feature that appears to be conserved in both FAM118B and its paralog FAM118A across vertebrates. While human FAM118B and FAM118A have individually very weak NAD-processing activity in vitro, their interaction leads to markedly increased activity, suggesting a tightly regulated system. The overexpression of wild-type human FAM118B and FAM118A leads to strongly decreased NAD levels in human cells, an effect that is abolished in catalytically dead or filament-deficient mutants. Our study highlights filament formation and NAD processing as conserved mechanisms among immunity-associated sirtuins across evolution.
History
DepositionApr 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FAM118B
B: Protein FAM118B
C: Protein FAM118B
D: Protein FAM118B
E: Protein FAM118B


Theoretical massNumber of molelcules
Total (without water)208,6225
Polymers208,6225
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
Protein FAM118B


Mass: 41724.402 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: 6xHis-tag with additional residue before and after the tag: MGSSHHHHHHSSGLVPRGSH
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM118B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPY3
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: homopolymer/filament of human FAM118B / Type: COMPLEX / Details: filament purified from E. coli / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP and 12.5 m Tris pH 7.5, 150 mM NaCl, 0.5 mM TCEP, the sample was originally in the Hepes buffer and prior to vitrification it was diluted in the ...Details: 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP and 12.5 m Tris pH 7.5, 150 mM NaCl, 0.5 mM TCEP, the sample was originally in the Hepes buffer and prior to vitrification it was diluted in the Tris buffer in 1:3 volume ratio, respectively to a final concentration of protein at 0.1 mg/mL (3.5 uM)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)piperazine-1-ethane-sulfonic acidHEPES1
2150 mMsodim chlorideNaCl1
30.5 mMtris(2-carboxyethyl)phosphineTCEP1
412.5 mMTris(hydroxymethyl)aminomethaneTRIS1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: the sample was purified in the form of filaments of various sizes ranging from about 3 to 10 units
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291.15 K
Details: A 3.5 uL of sample was applied to the holey carbon side of the grid. Without an additional incubation time, the grid was back blotted once for 1.5 s and plunge frozen in liquid 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: 2600 nm / Nominal defocus min: 1600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11630 / Details: Grid ID 6-1-db251124
EM imaging opticsDetails: Gatan K3 direct electron detector with energy filter was used
Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selectionpatch CTF estimation
2EPUimage acquisition
4cryoSPARC4.5.3CTF correctionpatch motion correction default settings
7UCSF ChimeraX1.9model fitting
9ISOLDE1.7model refinement
10cryoSPARC4.5.3initial Euler assignment
11cryoSPARC4.5.3final Euler assignment
12cryoSPARC4.5.3classification
13cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1958302
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111156 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Molecular dynamics flexible fitting was used in ISOLDE/Chimerax
Atomic model buildingAccession code: Q9BPY3F1 / Chain residue range: 28-326 / Source name: AlphaFold / Type: in silico model

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