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- EMDB-53555: Human FAM118B(34-334) 2 protomers -

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Basic information

Entry
Database: EMDB / ID: EMD-53555
TitleHuman FAM118B(34-334) 2 protomers
Map data
Sample
  • Complex: Human FAM118B(24-334) focused trimer filament
    • Protein or peptide: Protein FAM118B
KeywordsNADase / HYDROLASE
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: 4.8 Å
AuthorsMissoury S / Coste F / Baretic D / Patel K / Delarue M / Ahel I / Suskiewicz MJ
Funding support1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53555.png

Downloads & links

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Map

FileDownload / File: emd_53555.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 429.568 Å		0.84 Å/pix.
x 512 pix.
= 429.568 Å		0.84 Å/pix.
x 512 pix.
= 429.568 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-4.426873 - 6.339996
Average (Standard dev.)0.00050884753 (±0.027110912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 429.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53555_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53555_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 FAM118B(24-334) focused trimer filament

EntireName: Human FAM118B(24-334) focused trimer filament
Components
  • Complex: Human FAM118B(24-334) focused trimer filament
    • Protein or peptide: Protein FAM118B

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Supramolecule #1: Human FAM118B(24-334) focused trimer filament

SupramoleculeName: Human FAM118B(24-334) focused trimer filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein FAM118B

MacromoleculeName: Protein FAM118B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.08716 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PRKLLPSLKT KKPRELVLVI GTGISAAVAP QVPALKSWKG LIQALLDAAI DFDLLEDEES KKFQKCLHED KNLVHVAHDL IQKLSPRTS NVRSTFFKDC LYEVFDDLES KMEDSGKQLL QSVLHLMENG ALVLTTNFDN LLELYAADQG KQLESLDLTD E KKVLEWAQ ...String:
PRKLLPSLKT KKPRELVLVI GTGISAAVAP QVPALKSWKG LIQALLDAAI DFDLLEDEES KKFQKCLHED KNLVHVAHDL IQKLSPRTS NVRSTFFKDC LYEVFDDLES KMEDSGKQLL QSVLHLMENG ALVLTTNFDN LLELYAADQG KQLESLDLTD E KKVLEWAQ EKRKLSVLHI HGVYTNPSGI VLHPAGYQNV LRNTEVMREI QKLYENKSFL FLGCGWTVDD TTFQALFLEA VK HKSDLEH FMLVRRGDVD EFKKLRENML DKGIKVISYG DDYADLPEYF KRLTCEISTR G

UniProtKB: Protein FAM118B

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8.8 / Details: 25 mM Tris, pH 8.8, 250 mM NaCl, 0.5 mM TCEP
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 289000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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