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- EMDB-55134: P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation) -

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Basic information

Entry
Database: EMDB / ID: EMD-55134
TitleP. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)
Map data
Sample
  • Complex: P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)
    • Protein or peptide: Dehydrogenase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywords70S / ribosome / Hibernation / Pyrococcus abyssi
Function / homologyUncharacterised conserved protein, 2xCBS, MJ1404 type / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / CBS domain-containing protein
Function and homology information
Biological speciesPyrococcus abyssi GE5 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMadru CM / Bourgeois GB / Mechulam YM / Schmitt ES
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Nat Commun / Year: 2026
Title: A family of ribosome hibernation factors widespread in Archaea.
Authors: Clément Madru / Gabrielle Bourgeois / Rémi Dulermo / Régine Capeyrou / Gwendoline Joncour / Karima Figuigui / Magalie Duchateau / Julia Chamot-Rooke / Claire Duboc / Stéphane l'Haridon / ...Authors: Clément Madru / Gabrielle Bourgeois / Rémi Dulermo / Régine Capeyrou / Gwendoline Joncour / Karima Figuigui / Magalie Duchateau / Julia Chamot-Rooke / Claire Duboc / Stéphane l'Haridon / Logan Mc Teer / Marta Kwapisz / Béatrice Clouet-d'Orval / Marie Bouvier / Yves Mechulam / Guillaume Borrel / Emmanuelle Schmitt / Didier Flament /
Abstract: Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Using cryo-EM analysis, we studied hibernation pathways in Pyrococcus abyssi ...Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Using cryo-EM analysis, we studied hibernation pathways in Pyrococcus abyssi stressed cells. We identified HibA, a previously unrecognized family of hibernation factors widespread in Archaea. HibA consists of a bacterial-like HPF/RaiA domain fused to a Cystathionine Beta Synthase module. Unexpectedly, HibA binds to the ribosome in three different conformations, occupying the A, P and E sites of tRNAs, as well as that of mRNA, enhancing its ability to protect the ribosome from degradation. Idle ribosomes also frequently accumulate the archaeal homolog of eukaryotic ribosome maturation protein SBDS (aSBDS), suggesting that stressed archaeal cells may engage parallel hibernation routes in which aSBDS can complement HibA. Deletion of hibA in Thermococcus barophilus delays recovery from stationary phase and reduces 70S ribosome pools, establishing its role in ribosome preservation. Taxonomic profiling shows that many archaeal lineages encode distinct repertoires of ribosome-associated protection factors, underscoring the modular and multi-layered nature of archaeal hibernation systems. In addition, a comprehensive phylogenetic analysis highlights the evolutionary relationships between prevalent ribosome hibernation factors across Bacteria and Archaea.
History
DepositionSep 24, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55134.png

Downloads & links

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Map

FileDownload / File: emd_55134.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.13853355 - 0.40651357
Average (Standard dev.)0.004732008 (±0.02554355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55134_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55134_half_map_2.map
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Sample components

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Entire : P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)

EntireName: P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)
Components
  • Complex: P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)
    • Protein or peptide: Dehydrogenase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)

SupramoleculeName: P. abyssi hibernation factor Hib bound to ATP (Hib-PTC conformation)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Macromolecule #1: Dehydrogenase

MacromoleculeName: Dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 44.583812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVGIQVQEVM TDRYAKIDIN APLSEAIGII EKEDPDLILV FDDNVYKGVL TQDLIIRSHL KWDPTKAKVR DVYKPAPVVK PTDDLSHAA KLLLETDLRS LPVGENKAEI LGVISDMALL ERVVAEEFGK RKVEEFMTKD VITLGPDDTV AKALATMRDH G ISRIPVVD ...String:
MVGIQVQEVM TDRYAKIDIN APLSEAIGII EKEDPDLILV FDDNVYKGVL TQDLIIRSHL KWDPTKAKVR DVYKPAPVVK PTDDLSHAA KLLLETDLRS LPVGENKAEI LGVISDMALL ERVVAEEFGK RKVEEFMTKD VITLGPDDTV AKALATMRDH G ISRIPVVD EEGKLEGLVT LHDLIIRFIK PRFKAQYGEL AGEKIPPFSM KLREAMIKGV ITIMPEATIR EAVSTMKDNN ID GLVVVDE NNKVVGILTV KDLLLPISRM VEKEARFYLQ LGGDASALSE FTRERIINDI KRFVDGYADL LGNEGIIYLY IRR FNEKFR GVHLYQARMR VVTDRGVFIA RGETWGAIQA VHDAIRAIER QLLQKAELER DIRYAKRFIE KLELWR

UniProtKB: CBS domain-containing protein

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 20409
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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