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- EMDB-55140: Cryo-EM structure of the N-terminal domain of Hib bound to the L1... -

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Basic information

Entry
Database: EMDB / ID: EMD-55140
TitleCryo-EM structure of the N-terminal domain of Hib bound to the L1 stalk of Pyrococcus abyssi 70S
Map data
Sample
  • Complex: Cryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor Hib (Hib PTC conformation with E-site tRNA)
    • RNA: rRNA 23S
    • Protein or peptide: Dehydrogenase
    • Protein or peptide: Large ribosomal subunit protein uL1
Keywords70S / ribosome / 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
Large ribosomal subunit protein uL1 / CBS domain-containing protein
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_55140.png

Downloads & links

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Map

FileDownload / File: emd_55140.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

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: 0.029
Minimum - Maximum-0.1741717 - 0.31991738
Average (Standard dev.)-0.0005809432 (±0.0049308864)
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: #2

Fileemd_55140_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_55140_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of P. abyssi 70S ribosome in complex with hiber...

EntireName: Cryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor Hib (Hib PTC conformation with E-site tRNA)
Components
  • Complex: Cryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor Hib (Hib PTC conformation with E-site tRNA)
    • RNA: rRNA 23S
    • Protein or peptide: Dehydrogenase
    • Protein or peptide: Large ribosomal subunit protein uL1

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Supramolecule #1: Cryo-EM structure of P. abyssi 70S ribosome in complex with hiber...

SupramoleculeName: Cryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor Hib (Hib PTC conformation with E-site tRNA)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)

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Macromolecule #1: rRNA 23S

MacromoleculeName: rRNA 23S / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 985.295438 KDa
SequenceString: CGAGGGCUCG GGUAGAAGAC C(4AC)GGUUGAUG GGGCGGGGAU GUAAGCGGGA AGGGUCAAC(4AC) GACCCGCUUA GU CUGCCGC CCCCAAUCGC C(4AC)GAGGGCCU GGCCCCUCCG GUAGGGGGUC AGGACACUAA GCCGCC(4AC)GGU GGAUG GCUC GGCUCGGGGC ...String:
CGAGGGCUCG GGUAGAAGAC C(4AC)GGUUGAUG GGGCGGGGAU GUAAGCGGGA AGGGUCAAC(4AC) GACCCGCUUA GU CUGCCGC CCCCAAUCGC C(4AC)GAGGGCCU GGCCCCUCCG GUAGGGGGUC AGGACACUAA GCCGCC(4AC)GGU GGAUG GCUC GGCUCGGGGC GC(4AC)GACGAAG GGCGUGGCAA GCUGCGAUAA GCCCCGGCGA GGCGCAGGCA GC(4AC)GUCGA A CCGGGGAUUC C(4AC)GAAUGGGA CCUCC(4AC)GCGG CUUAUGCCGC ACUCCGGGGC AUAAGCCCCG GAGGGGGAAC G CGGGGAAU UGAAACAUCU UAGUACC(4AC)GC AGGAAAAGAA A(OMG)CAAAAGCG AUGC(4AC)GUGAG UAGGGGCGAC (4AC)GAAAGCGG CACAGGGCAA ACUGAACCCC GGGCCGACGA GGUUCGGGGG AUGUGGGGUU GUAGGGCCCC CGUAUGA GA CCCUCGCGGG UGAAGC(4AC)GAA GUC(4AC)GCUGGA ACGCGGCGCC GGAGAGGGUG AUAGCCCCGU AGGCGUAAGC CCGCAGGGU CUCGGGGGAC CCUGAGUAC(4AC) GUCGGUUGGA UAUCCGGCGG GAAGCUGGGA GGCAUCGGCU CCCAACC CU AAAUACGUCC CGAGACCGAU AGCGAACUAG UA(OMC)(LHH)GUGAGG GAAAGCUGAA AAGCACCC(4AC)G GGAGGG GGG UGAAAAGAGC CUGAAACCGG GCGGCGAUAG GAGGGUGCGG CC(4AC)GAAAGGA AUGAGCCUCC CCGAAGGAAA CCG CGGCGA CGCGGGAGUA CGAGGGGAGG GGACCGGGGU UGCACCGUCC GUCUUGAAAC ACGGGGCA(OMG)G GAGUUCGCGG C(4AC)GUGGCGA GGUUAAGGGG GUUAAGCCC(4AC) GUAGC(4AC)GCAG GGAAACCGAC AUGCCCGCAG CCGGGCCUC GAGCCCGGUG AGGGGCGGGG UGCGAAAGCG CCCGGAGUCA CGGCCGCGAG ACC(4AC)(OMG)AAACC GGUCGAUCUA GC CCGGGGC AGGGUGAAGU CCCUCAACAG AGGGAUGGAG GCC(4AC)GCUAGG GGUGCUGAUG UGCAGUUCGC UCCCGUGAC CCCGGGCUAG GGGUGAAAGG CCAAUCGAGG C(4AC)GGAGAU(A2M)G CUGGUUCC(4AC)G C(4AC)GAAUCAUC CCGC AGGAU GGCCUCCCCG GAGGUAGGCG GUGGGGUAGA GCACUGAUUG GGGGUGCAGG GGGCGAAAGC CCCCGGCCCC CUGUC AAAC UCCGAACCCA CCGCCGCCGU AGAUGGGGGG AGUAGGGUGG CGGUGUAAGC CGUCCAC(4AC)GA GAGGGGAACA AC CCAGAC(4AC) GGGGUUAAGG CCCCAAAGUG CCGGCUAAGU GUUACUCCAA AGGGUGUCC(4AC) GGGCCUUAGA CAGCG GGGA GGUAGGCUUA GAAGCAGCCA UCCUUUAAAG AGUGCGUAAC AGCUCACCCG UCGAGGUCCG GGGCCCCGAA AAUGGA CGG GGCUCAAGCC GGCCGCCGAG ACCCCGGCGC ACGGACCGAU UGGUCCGUGA UCGGGUAGGC GGGCGUGC(4AC)G GUG GCGUAG AAGCCGGGCC GUAAGGUCCG GUGGAGCCGC CGGUAUCGCG GAUCCUGCCG GGAGUAGCAG CGUAGUCGGG UGAG AAUCC (4AC)GAC(4AC)GC(4AC)GG AGGGGCCAGG GUUCCACAGG CAAUGGUCGU CAGC(4AC)GUGGG UUAGUCGGU CCUAACCC(4AC)G CC(4AC)GUAACUC GGCGCGGGGG AAAGGGAAAC GGGUUAAUAU UCC(4AC)GUAC(4AC)G CGGG GGUAG GUGCGGCAAC GCAAGCC(4AC)GG AGGGUGACGC CUCGGGGUAG GCGGACCGGC CGAUGAGGCC GGCUAAGCGU A UAAGCC(4AC)G GGGAGUGC(4AC)G UAAUGGCGAG AAC(4AC)GGGUGA AAGCGCGAAU GGCCCCCCCG UUAGGGGGGU UCCGCCGAU CCCUGGGGCC CGUGAAAAGC CCUCCGGGAA UUCCGAUCCC C(4AC)GCGAC(4AC)GU AC(4AC)GAGAAC (4AC)GACACAGGU GCCCCUGGGU GAGAAGCCUA AGGCGUGUCG GGGGAAACC(4AC) GGC(4AC)GAGGGA ACU(OMC) GGCAA ACUGGCCC(4AC)G UAACUUCGGG AGAAGGGGUG CCUGCGGGUG CGUAACCCGC AGGUCGCAGU GACUAGGGGG G CC(4AC)GACUG UUUAAUAAAA ACACAGGUCC CAGCUAGCC(4AC) GAAAGGGUUU GUACUGGGGC (4AC)GACGCCUGC (5MC)CAGUGCCG GUAUGUGAAG CCCGGGUACA ACCGGGUGAA GCAC(4AC)G(OMG)UAA AC(OMG)GC(OMG)GGGG U AACUAUAA C(5MC)(5MC)UCUUAAG GU(A2M)GCGAAAU UC(5MC)UUGUCGG UUAAAUG(5MC)CG AC(5MC)UGCAU G AAUGGCGUAA CGAGGUCCCC GCUGUCCCCG GCCGGGGCC(4AC) GGCGAAACCU CUGCCUGGCG CGCAUGCCAG GGACC CC(4AC)G GUGGGAAGCG AAGACCCCAU GGAGCUUUAC UGCAGCCUGC (4AC)GUUGCCACG CGGCGGGGGG UGCGCAGC G UAGGCGGGAG GCGUCGAAGC CCGGCCUCCG GGUCGGGUGG AGCCGUCCAU GAGACACCGC CCACUCCUCG CCGCGUGGC UAACCCCCGA AAGGGGGGAC AGCGGUAGGU GGGCAGUUUG GCUGGGGCGG CACGCCCC(4AC)G AAAAGGUAUC GGGGGC GCC CUAAGGUCGG CUCAGGCGGG UCAGGAAUC(4AC) GC(4AC)GUAGAGU GCAAGGGCAA AAGC(4AC)GGCCU GACUG GACC (4AC)GUAACAGAG GCGGGUCCAG CCC(4AC)GAAAGG GUGGCCUAGC GAACCCCUGU GCCUCCC(4AC)GG UGGG GGCCA GGGAUGACAG AAAAGCUACC CUGG(OMG)GAUAA CAGAGUCGUC UCGGGCGAGA GCCCAUAUCG ACCC(4AC)GA GG CUUGCUACCU (5MC)GCUGUCGGC UCUUCCCAUC CUGGCCCUGC AGCAGGGGCC AAGGGUGGGG G(OMU)GUUCACCC AUUAAAGGG GAACGUGAGC UGGGUUUAGA CCGUCGUGAG ACAGGUCGGA UGCUAUCUAC CGGGGGUGUU GGC(4AC)GCC UG AGGGGAAGGU GCCCUUAGUA CGAGAGGAAC AGGGCGC(4AC)GC GGCCUCUGGU CUAC(4AC)GGUUG UCCUCC (4AC)GG GCAUCGCCGG GCAGCUACGC (4AC)GCAGC(4AC)GAU AAGGCCUGAA GGCAUCUAAG GC(4AC)GAAGCGG C CCC(4AC)GAAA AUAGGCGGCC GUU

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Macromolecule #2: Dehydrogenase

MacromoleculeName: Dehydrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 44.583812 KDa
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 #3: Large ribosomal subunit protein uL1

MacromoleculeName: Large ribosomal subunit protein uL1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi GE5 (archaea)
Molecular weightTheoretical: 24.370666 KDa
SequenceString: MSRMPFDRQK IVEAVKEAKA RAKPRNFTQS VEVAVNLKDI DLKRPENRFK LEVVLPHGRG KDVKIAVIAD GAVAEAARRL GLDVISSAE LEEIAQSPRQ ARKLAKKYDF FIAEAPLMPK IGRYLGKYLG PRNKMPVVVP PTMSNLEPIV EKLKKTVRIQ L KNNPVVHA ...String:
MSRMPFDRQK IVEAVKEAKA RAKPRNFTQS VEVAVNLKDI DLKRPENRFK LEVVLPHGRG KDVKIAVIAD GAVAEAARRL GLDVISSAE LEEIAQSPRQ ARKLAKKYDF FIAEAPLMPK IGRYLGKYLG PRNKMPVVVP PTMSNLEPIV EKLKKTVRIQ L KNNPVVHA PVGTEKMSDE EIAENIETVL NAIIGKLERG ESQIKSVYVK TTMGPAVKVK G

UniProtKB: Large ribosomal subunit protein uL1

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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: PDB ENTRY
PDB model - PDB ID:

7zah

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 170000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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