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- EMDB-53488: human FAM118B pentameric filament -

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Basic information

Entry
Database: EMDB / ID: EMD-53488
Titlehuman FAM118B pentameric filament
Map datasharpened map for pentameric filament of hFAM118B
Sample
  • Complex: homopolymer/filament of human FAM118B
    • Protein or peptide: Protein FAM118B
Keywordsfilament / enzyme / NAD / nucleus / innate immunity / sirtuin / IMMUNE SYSTEM
Function / homologyProtein FAM118 / SIR2-like domain / Cajal body / identical protein binding / Protein FAM118B
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsBaretic D / Missoury S / Patel K / Coste F / Delarue M / Suskiewicz JM / Ahel I
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53488.png

Downloads & links

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Map

FileDownload / File: emd_53488.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map for pentameric filament of hFAM118B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.25704774 - 0.5850272
Average (Standard dev.)-0.000020534328 (±0.006967291)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53488_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map for pentameric filament of hFAM118B

Fileemd_53488_additional_1.map
Annotationunsharpened map for pentameric filament of hFAM118B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map A for pentameric filament of hFAM118B

Fileemd_53488_half_map_1.map
Annotationhalf-map_A for pentameric filament of hFAM118B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B for pentameric filament of hFAM118B

Fileemd_53488_half_map_2.map
Annotationhalf-map_B for pentameric filament of hFAM118B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homopolymer/filament of human FAM118B

EntireName: homopolymer/filament of human FAM118B
Components
  • Complex: homopolymer/filament of human FAM118B
    • Protein or peptide: Protein FAM118B

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Supramolecule #1: homopolymer/filament of human FAM118B

SupramoleculeName: homopolymer/filament of human FAM118B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: filament purified from E. coli
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein FAM118B

MacromoleculeName: Protein FAM118B / type: protein_or_peptide / ID: 1
Details: 6xHis-tag with additional residue before and after the tag: MGSSHHHHHHSSGLVPRGSH
Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.724402 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASTGSQASD IDEIFGFFND GEPPTKKPRK LLPSLKTKKP RELVLVIGTG ISAAVAPQVP ALKSWKGLI QALLDAAIDF DLLEDEESKK FQKCLHEDKN LVHVAHDLIQ KLSPRTSNVR STFFKDCLYE VFDDLESKME D SGKQLLQS ...String:
MGSSHHHHHH SSGLVPRGSH MASTGSQASD IDEIFGFFND GEPPTKKPRK LLPSLKTKKP RELVLVIGTG ISAAVAPQVP ALKSWKGLI QALLDAAIDF DLLEDEESKK FQKCLHEDKN LVHVAHDLIQ KLSPRTSNVR STFFKDCLYE VFDDLESKME D SGKQLLQS VLHLMENGAL VLTTNFDNLL ELYAADQGKQ LESLDLTDEK KVLEWAQEKR KLSVLHIHGV YTNPSGIVLH PA GYQNVLR NTEVMREIQK LYENKSFLFL GCGWTVDDTT FQALFLEAVK HKSDLEHFML VRRGDVDEFK KLRENMLDKG IKV ISYGDD YADLPEYFKR LTCEISTRGT SAGMVREGQL NGSSAAHSEI RGCST

UniProtKB: Protein FAM118B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)piperazine-1-ethane-sulfonic acid
150.0 mMNaClsodim chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
12.5 mMTRISTris(hydroxymethyl)aminomethane

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)
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: LEICA EM GP
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..
Detailsthe sample was purified in the form of filaments of various sizes ranging from about 3 to 10 units

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Details: Gatan K3 direct electron detector with energy filter was used
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 11630 / Average electron dose: 43.7 e/Å2 / Details: Grid ID 6-1-db251124
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1958302
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3)
Software - details: patch motion correction default settings
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
In silico model: alphafold3 predicted filament of human FAM118B
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 111156
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 5 / Avg.num./class: 104000 / Software - Name: cryoSPARC (ver. 4.5.3)
Details: The fifth class (22% or 104000 particles) was discarded as junk particles.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

y3f1


Chain - Residue range: 28-326 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsMolecular dynamics flexible fitting was used in ISOLDE/Chimerax
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9r0s:
human FAM118B pentameric filament

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