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- PDB-9srf: Cryo-EM structure of the N-terminal domain of Hib bound to the L1... -

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Basic information

Entry
Database: PDB / ID: 9srf
TitleCryo-EM structure of the N-terminal domain of Hib bound to the L1 stalk of Pyrococcus abyssi 70S
Components
  • Dehydrogenase
  • Large ribosomal subunit protein uL1
  • rRNA 23S
KeywordsRIBOSOME / 70S / Hibernation / Pyrococcus abyssi
Function / homology
Function and homology information


regulation of translation / large ribosomal subunit / tRNA binding / rRNA binding / translation / structural constituent of ribosome
Similarity search - Function
Uncharacterised conserved protein, 2xCBS, MJ1404 type / Ribosomal protein L1, archaea / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. ...Uncharacterised conserved protein, 2xCBS, MJ1404 type / Ribosomal protein L1, archaea / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL1 / CBS domain-containing protein
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMadru, C.M. / Bourgeois, G.B. / Mechulam, Y.M. / Schmitt, E.S.
Funding support France, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: rRNA 23S
H: Dehydrogenase
BA: Large ribosomal subunit protein uL1


Theoretical massNumber of molelcules
Total (without water)1,054,2503
Polymers1,054,2503
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: RNA chain rRNA 23S


Mass: 985295.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)
#2: Protein Dehydrogenase


Mass: 44583.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UYR4
#3: Protein Large ribosomal subunit protein uL1 / 50S ribosomal protein L1


Mass: 24370.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UWR8
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: Cryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor Hib (Hib PTC conformation with E-site tRNA)
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 116.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00316016
ELECTRON MICROSCOPYf_angle_d0.58498589
ELECTRON MICROSCOPYf_chiral_restr0.04041071
ELECTRON MICROSCOPYf_plane_restr0.0035750
ELECTRON MICROSCOPYf_dihedral_angle_d21.91962961

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