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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 / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / 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 / Small zinc finger protein HVO_2753-like, Zn-binding pocket / 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 / Small zinc finger protein HVO_2753-like, Zn-binding pocket / 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. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein L44e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Zinc finger C2H2 type domain profile. / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S10, eukaryotic/archaeal / : / Ribosomal protein L30e signature 1. / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L35Ae, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L35Ae signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein S17e, conserved site / Ribosomal protein L40e superfamily / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S27a / Ribosomal protein S27a / : / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / : / Ribosomal protein L34Ae
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: 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- ...Authors: 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.
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
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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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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