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- PDB-9r3e: Human FAM118B(34-334) 2 protomers -

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Basic information

Entry
Database: PDB / ID: 9r3e
TitleHuman FAM118B(34-334) 2 protomers
ComponentsProtein FAM118B
KeywordsHYDROLASE / NADase
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: 4.8 Å
AuthorsMissoury, S. / Coste, F. / Baretic, D. / Patel, K. / Delarue, M. / Ahel, I. / Suskiewicz, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionMay 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
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Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein FAM118B
C: Protein FAM118B


Theoretical massNumber of molelcules
Total (without water)68,1742
Polymers68,1742
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: 34087.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human FAM118B(24-334) focused trimer filament / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.8 / Details: 25 mM Tris, pH 8.8, 250 mM NaCl, 0.5 mM TCEP
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
9PHENIX1.21.2_5419model refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 289000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 4.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0124880
ELECTRON MICROSCOPYf_angle_d1.546580
ELECTRON MICROSCOPYf_dihedral_angle_d6.421634
ELECTRON MICROSCOPYf_chiral_restr0.085748
ELECTRON MICROSCOPYf_plane_restr0.014836

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