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- PDB-9srd: Cryo-EM structure of P. abyssi 70S ribosome in complex with hiber... -

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Basic information

Entry
Database: PDB / ID: 9srd
TitleCryo-EM structure of P. abyssi 70S ribosome in complex with hibernation factor HibA (HibA-uL5 conformation)
Components
  • (30S ribosomal protein ...) x 25
  • (Large ribosomal subunit protein ...) x 32
  • 50S ribosomal protein L7Ae
  • C2H2-type domain-containing protein
  • Dehydrogenase
  • Small ribosomal subunit protein eS32
  • Zn-ribbon RNA-binding protein involved in translation
  • rRNA 16S
  • rRNA 23S
  • rRNA 5S
KeywordsRIBOSOME / 70S / Hibernation / Pyrococcus abyssi
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / large ribosomal subunit / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis ...ribonuclease P activity / tRNA 5'-leader removal / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / large ribosomal subunit / ribosomal small subunit assembly / ribosome biogenesis / ribosomal small subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Uncharacterised conserved protein, 2xCBS, MJ1404 type / Ribosomal protein L14e / : / : / Ribosomal protein L14, KOW motif / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Ribosomal protein aS21 / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal ...Uncharacterised conserved protein, 2xCBS, MJ1404 type / Ribosomal protein L14e / : / : / Ribosomal protein L14, KOW motif / Small zinc finger protein HVO_2753-like, zinc-binding pocket / Small zinc finger protein HVO_2753-like / Ribosomal protein aS21 / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / : / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L32e, archaeal / : / : / Ribosomal protein L7Ae, archaea / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / : / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L23 / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / zinc finger / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Zinc finger C2H2 type domain profile. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L10e / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / : / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein S27a / Ribosomal protein L30e, conserved site / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L13, eukaryotic/archaeal
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / C2H2-type domain-containing protein / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein involved in translation / C2H2-type domain-containing protein / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein eS24 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL39 / Dehydrogenase / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL5 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL43 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsMadru, C. / Bourgeois, G. / Mechulam, Y. / Schmitt, E.
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 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 2.0Jun 24, 2026Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / em_admin / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _em_admin.last_update / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 1.1Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: rRNA 23S
2: rRNA 16S
3: rRNA 5S
AA: 30S ribosomal protein S3Ae
AB: 30S ribosomal protein S2
AC: Zn-ribbon RNA-binding protein involved in translation
AD: 30S ribosomal protein S4
AE: 30S ribosomal protein S4e
AF: 30S ribosomal protein S5
AG: 30S ribosomal protein S6e
AH: 30S ribosomal protein S7
AI: 30S ribosomal protein S8
AJ: 30S ribosomal protein S8e
AK: 30S ribosomal protein S9
AL: 30S ribosomal protein S10
AM: 30S ribosomal protein S11
AN: 30S ribosomal protein S12
AP: 30S ribosomal protein S14 type Z
AQ: 30S ribosomal protein S15
AR: 30S ribosomal protein S17
AS: 30S ribosomal protein S17e
AU: 30S ribosomal protein S19e
AV: 30S ribosomal protein S24e
AW: 30S ribosomal protein S27e
AX: 30S ribosomal protein S28e
AY: 30S ribosomal protein S27ae
AZ: 30S ribosomal protein S3
A0: Small ribosomal subunit protein eS32
A3: 50S ribosomal protein L7Ae
AT: 30S ribosomal protein S19
AO: 30S ribosomal protein S13
BB: Large ribosomal subunit protein uL2
BY: Large ribosomal subunit protein uL30
BO: Large ribosomal subunit protein uL18
BC: Large ribosomal subunit protein uL3
B5: Large ribosomal subunit protein eL14
BL: Large ribosomal subunit protein uL15
Bf: Large ribosomal subunit protein eL39
BU: Large ribosomal subunit protein uL24
Bb: Large ribosomal subunit protein eL32
Be: Large ribosomal subunit protein eL37
BE: Large ribosomal subunit protein uL5
Ba: Large ribosomal subunit protein eL31
BT: Large ribosomal subunit protein uL23
BW: Large ribosomal subunit protein uL29
Bi: Large ribosomal subunit protein eL43
BI: Large ribosomal subunit protein uL13
BR: Large ribosomal subunit protein eL21
BK: Large ribosomal subunit protein eL14
BQ: Large ribosomal subunit protein eL19
BV: Large ribosomal subunit protein eL24
Bj: Large ribosomal subunit protein eL42
BG: 50S ribosomal protein L7Ae
BD: Large ribosomal subunit protein uL4
BF: Large ribosomal subunit protein uL6
BZ: Large ribosomal subunit protein eL30
B6: 30S ribosomal protein S24e
BP: Large ribosomal subunit protein eL18
BM: Large ribosomal subunit protein eL15
BS: Large ribosomal subunit protein uL22
Bd: Large ribosomal subunit protein eL34
BN: Large ribosomal subunit protein uL16
Bg: Large ribosomal subunit protein eL40
Bc: Large ribosomal subunit protein eL33
BJ: Large ribosomal subunit protein uL14
Bl: Large ribosomal subunit protein eL20
B4: 50S ribosomal protein L7Ae
Bk: C2H2-type domain-containing protein
H: Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,541,081326
Polymers2,534,30069
Non-polymers6,781257
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

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RNA chain , 3 types, 3 molecules 123

#1: RNA chain rRNA 23S


Mass: 984301.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)
#2: RNA chain rRNA 16S


Mass: 492728.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)
#3: RNA chain rRNA 5S


Mass: 41443.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea)

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30S ribosomal protein ... , 25 types, 26 molecules AAABADAEAFAGAHAIAJAKALAMANAPAQARASAUAVB6AWAXAYAZATAO

#4: Protein 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 22888.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V2K7
#5: Protein 30S ribosomal protein S2


Mass: 23026.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V191
#7: Protein 30S ribosomal protein S4


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61992
#8: Protein 30S ribosomal protein S4e


Mass: 28246.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U8
#9: Protein 30S ribosomal protein S5


Mass: 26523.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V5
#10: Protein 30S ribosomal protein S6e


Mass: 14029.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UYS3
#11: Protein 30S ribosomal protein S7


Mass: 24662.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V109
#12: Protein 30S ribosomal protein S8


Mass: 14772.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V0
#13: Protein 30S ribosomal protein S8e


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UZL4
#14: Protein 30S ribosomal protein S9


Mass: 15293.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V195
#15: Protein 30S ribosomal protein S10


Mass: 11795.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V0V6
#16: Protein 30S ribosomal protein S11


Mass: 14772.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62010
#17: Protein 30S ribosomal protein S12


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61994
#18: Protein 30S ribosomal protein S14 type Z


Mass: 6644.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62012
#19: Protein 30S ribosomal protein S15


Mass: 18697.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V2K9
#20: Protein 30S ribosomal protein S17


Mass: 13364.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U5
#21: Protein 30S ribosomal protein S17e


Mass: 8059.528 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V0G0
#22: Protein 30S ribosomal protein S19e


Mass: 17422.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V0G8
#23: Protein 30S ribosomal protein S24e


Mass: 11798.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UY20
#24: Protein 30S ribosomal protein S27e


Mass: 7186.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UXZ3
#25: Protein 30S ribosomal protein S28e


Mass: 8102.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61029
#26: Protein 30S ribosomal protein S27ae


Mass: 5992.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P61238
#27: Protein 30S ribosomal protein S3


Mass: 23472.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U1
#30: Protein 30S ribosomal protein S19


Mass: 15307.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1T9
#31: Protein 30S ribosomal protein S13


Mass: 16992.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1A0

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Protein , 4 types, 6 molecules ACA3BGB4BkH

#6: Protein Zn-ribbon RNA-binding protein involved in translation


Mass: 7163.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: G8ZFK7
#29: Protein 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13442.678 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62008
#64: Protein C2H2-type domain-containing protein


Mass: 7795.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: G8ZKB7
#65: 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

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Protein/peptide , 1 types, 1 molecules A0

#28: Protein/peptide Small ribosomal subunit protein eS32 / 50S ribosomal protein L41e / Large ribosomal subunit protein eL41


Mass: 5023.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q8U232

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Large ribosomal subunit protein ... , 32 types, 33 molecules BBBYBOBCB5BKBLBfBUBbBeBEBaBTBWBiBIBRBQBVBjBDBFBZBPBMBSBdBNBg...

#32: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 26202.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1T8
#33: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 17745.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V6
#34: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 23308.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V4
#35: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 40928.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1T5
#36: Protein Large ribosomal subunit protein eL14 / 50S ribosomal protein L14e


Mass: 8913.618 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UZJ5
#37: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 16360.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V7
#38: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6316.794 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UYI8
#39: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 14420.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U7
#40: Protein Large ribosomal subunit protein eL32 / 50S ribosomal protein L32e


Mass: 15660.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V2
#41: Protein Large ribosomal subunit protein eL37 / 50S ribosomal protein L37e


Mass: 7321.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62004
#42: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 21549.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U9
#43: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 11052.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UYI7
#44: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 9893.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1T7
#45: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8182.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U2
#46: Protein Large ribosomal subunit protein eL43 / 50S ribosomal protein L37Ae / Ribosomal protein L43e


Mass: 9005.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V202
#47: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16317.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V196
#48: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11408.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UZP1
#49: Protein Large ribosomal subunit protein eL19 / 50S ribosomal protein L19e


Mass: 18240.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V3
#50: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 8135.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V0W3
#51: Protein Large ribosomal subunit protein eL42 / 50S ribosomal protein L44e


Mass: 11274.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UXZ2
#52: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 28758.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1T6
#53: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 20736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1V1
#54: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10751.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V112
#55: Protein Large ribosomal subunit protein eL18 / 50S ribosomal protein L18e


Mass: 13839.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V197
#56: Protein Large ribosomal subunit protein eL15 / 50S ribosomal protein L15e


Mass: 22657.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V0D2
#57: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 17834.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U0
#58: Protein Large ribosomal subunit protein eL34 / 50S ribosomal protein L34e


Mass: 10935.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UZJ7
#59: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 20923.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UYU9
#60: Protein Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 5900.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62006
#61: Protein Large ribosomal subunit protein eL33 / 50S ribosomal protein L35Ae


Mass: 9755.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1P2
#62: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 15318.956 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9V1U6
#63: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX / LXA


Mass: 9364.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: Q9UYI5

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Non-polymers , 2 types, 257 molecules

#66: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 244 / Source method: obtained synthetically / Formula: Mg
#67: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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 HibA (HibA-uL5 conformation)
Type: RIBOSOME / Entity ID: #1-#65 / Source: NATURAL
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: 800 nm / Nominal defocus min: 300 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: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207000 / Symmetry type: POINT
Atomic model buildingSource name: Other / Type: other
RefinementHighest resolution: 2.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004183260
ELECTRON MICROSCOPYf_angle_d0.571270365
ELECTRON MICROSCOPYf_dihedral_angle_d21.99699164
ELECTRON MICROSCOPYf_chiral_restr0.03833380
ELECTRON MICROSCOPYf_plane_restr0.00516881

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