9SR9 | pdb_00009sr9

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

• PDB DOI: https://doi.org/10.2210/pdb9SR9/pdb
• EM Map EMD-55134: EMDB EMDataResource

• Classification: RIBOSOME
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-24 Released: 2026-08-12 
• Deposition Author(s): Madru, C.M., Bourgeois, G.B., Mechulam, Y.M., Schmitt, E.S.
• Funding Organization(s): Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A family of ribosome hibernation factors widespread in Archaea.

Madru, C., Bourgeois, G., Dulermo, R., Capeyrou, R., Joncour, G., Figuigui, K., Duchateau, M., Chamot-Rooke, J., Duboc, C., l'Haridon, S., Mc Teer, L., Kwapisz, M., Clouet-d'Orval, B., Bouvier, M., Mechulam, Y., Borrel, G., Schmitt, E., Flament, D.

(2026) Nat Commun 17

• PubMed: 42045235 
• DOI: https://doi.org/10.1038/s41467-026-72341-8
• Primary Citation Related Structures: 
  9SR9, 9SRA, 9SRB, 9SRC, 9SRD, 9SRE, 9SRF, 9T7H


• PubMed 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 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.

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Organizational Affiliation: 
• Structural Biology of the Cell, BIOC, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France.
Univ Brest, Ifremer, Biology and Ecology of Deep Marine Ecosystems (BEEP), 29280, Plouzané, France.
University of Toulouse, CNRS, CBI, Toulouse, France.
Proteomics Platform, Mass Spectrometry for Biology Unit, Institut Pasteur, Université de Paris-Cité, CNRS USR 2000, 75015, Paris, France.
Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, 75015, Paris, France. [e-mail].
Structural Biology of the Cell, BIOC, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120, Palaiseau, France. [e-mail].
Univ Brest, Ifremer, Biology and Ecology of Deep Marine Ecosystems (BEEP), 29280, Plouzané, France. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 45.09 kDa 
• Atom Count: 3,105 
• Modeled Residue Count: 386 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase	A [auth H]	392	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: PAB0961
UniProt
Find proteins for Q9UYR4 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9UYR4  Go to UniProtKB:  Q9UYR4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	B [auth H]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Madru, C.M., Bourgeois, G.B., Mechulam, Y.M., Schmitt, E.S.

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Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	--

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release