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- PDB-9qf5: Structure of P. furiosus 70S ribosome grown at 102deg -

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Basic information

Entry
Database: PDB / ID: 9qf5
TitleStructure of P. furiosus 70S ribosome grown at 102deg
Components
  • (Large ribosomal subunit protein ...) x 33
  • (Small ribosomal subunit protein ...) x 25
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • C2H2-type domain-containing protein
  • Zn-ribbon RNA-binding protein
KeywordsRIBOSOME / RNA modification / cryo-EM
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 / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...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 / rRNA processing / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / 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
Ribosomal protein L14e / : / 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 L14, KOW motif / Ribosomal protein L40e, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal ...Ribosomal protein L14e / : / 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 L14, KOW motif / 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 L19e, 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 / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / Zinc finger, C2H2 type / TRASH domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / zinc finger / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L44e signature. / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S3Ae, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae signature. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein 60S L18 and 50S L18e / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L35Ae, conserved site / : / Ribosomal protein L35Ae signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / : / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / 60S ribosomal protein L19 / Ribosomal S17
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Zn-ribbon RNA-binding protein / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL43 / 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 uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein eL37 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL40 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS8 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS32 / Large ribosomal subunit protein eL15 / C2H2-type domain-containing protein / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsMatzov, D. / Georgeson, J. / Westhof, E. / Schwartz, S. / Shalev-Benami, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-Discovery24433European Union
CitationJournal: Cell / Year: 2025
Title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome.
Authors: Miguel A Garcia-Campos / Joe Georgeson / Ronit Nir / Robert Reichelt / Kristin A Fluke / Donna Matzov / Vinithra Iyer / Brett W Burkhart / Lauren Lui / Anatoly Kustanovich / Felix ...Authors: Miguel A Garcia-Campos / Joe Georgeson / Ronit Nir / Robert Reichelt / Kristin A Fluke / Donna Matzov / Vinithra Iyer / Brett W Burkhart / Lauren Lui / Anatoly Kustanovich / Felix Grünberger / Supuni Thalalla-Gamage / Shereen A Howpay-Manage / Milan Gerovac / Nicolas Alexandre / Yuko Nobe / Jakub S Nowak / Manoj Perera / Alexander Apostle / Shiyue Fang / Sebastian Glatt / Ghil Jona / Sébastien Ferreira-Cerca / Jörg Vogel / Masato Taoka / Jordan L Meier / Eric Westhof / Thomas J Santangelo / Dina Grohmann / Moran Shalev-Benami / Schraga Schwartz /
Abstract: Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We ...Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We develop Pan-Mod-seq, permitting inference of 16 distinct modifications across dozens of samples in parallel. We applied Pan-Mod-seq to RNA from 14 species spanning all domains of life, cultured under highly diverse conditions. While dynamic modifications are rare in mesophiles, in extreme hyperthermophiles, ∼50% of modifications are dynamic. We dissect the biogenesis and function of a conserved module of tandem mC-acC modifications, co-induced at high temperatures, via enzymes intrinsically regulated by temperature and required for growth at higher temperatures. Cryo-electron microscopy (cryo-EM) structures of ribosomes from wild-type (WT) and enzyme-deficient archaea reveal recurrent molecular interactions through which they confer structural stability, and biophysical studies demonstrate their synergistic thermostabilizing role. Our findings systematically dissect rRNA modification plasticity and pave the way for surveying the rRNA epitranscriptome in health and disease.
History
DepositionMar 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A1: 16S rRNA
Aa: Small ribosomal subunit protein uS2
Ab: Small ribosomal subunit protein uS3
Ac: Small ribosomal subunit protein eS1
Ad: Small ribosomal subunit protein uS4
Ae: Small ribosomal subunit protein eS4
Af: Small ribosomal subunit protein uS5
Ag: Small ribosomal subunit protein eS6
Ah: Small ribosomal subunit protein uS7
Ai: Small ribosomal subunit protein uS8
Aj: Small ribosomal subunit protein eS8
Ak: Small ribosomal subunit protein uS9
Al: Small ribosomal subunit protein uS10
Am: Small ribosomal subunit protein uS11
An: Small ribosomal subunit protein uS12
Ao: Small ribosomal subunit protein uS13
Ap: Small ribosomal subunit protein uS14
Aq: Small ribosomal subunit protein uS15
Ar: Small ribosomal subunit protein uS17
As: Small ribosomal subunit protein eS17
At: Small ribosomal subunit protein uS19
Au: Small ribosomal subunit protein eS19
Av: Small ribosomal subunit protein eS24
Aw: Small ribosomal subunit protein eS27
Ax: Small ribosomal subunit protein eS28
Ay: Zn-ribbon RNA-binding protein
B1: 23S rRNA
B2: 5S rRNA
BA: Large ribosomal subunit protein uL2
BB: Large ribosomal subunit protein uL3
BC: Large ribosomal subunit protein uL4
BD: Large ribosomal subunit protein uL5
BE: Large ribosomal subunit protein uL6
BF: Large ribosomal subunit protein eL8
BG: Large ribosomal subunit protein eL8
BH: Large ribosomal subunit protein uL16
BI: Large ribosomal subunit protein uL13
BJ: Large ribosomal subunit protein uL14
BK: Large ribosomal subunit protein eL14
BL: Large ribosomal subunit protein eL14
BM: Large ribosomal subunit protein uL15
BN: Large ribosomal subunit protein eL15
BO: Large ribosomal subunit protein uL18
BP: Large ribosomal subunit protein eL18
BQ: Large ribosomal subunit protein eL19
BR: Large ribosomal subunit protein eL21
BS: Large ribosomal subunit protein uL22
BT: Large ribosomal subunit protein uL23
BU: Large ribosomal subunit protein uL24
BV: Large ribosomal subunit protein eL24
BW: Large ribosomal subunit protein uL29
BX: Large ribosomal subunit protein uL30
BY: Large ribosomal subunit protein eL30
BZ: Large ribosomal subunit protein eL31
Ba: Large ribosomal subunit protein eL32
Bb: Large ribosomal subunit protein eL34
Bc: Large ribosomal subunit protein eL33
Bd: Large ribosomal subunit protein eL37
Be: Large ribosomal subunit protein eL43
Bf: Large ribosomal subunit protein eL39
Bg: Large ribosomal subunit protein eL40
Bh: Small ribosomal subunit protein eS32
Bi: Large ribosomal subunit protein eL42
Bj: Large ribosomal subunit protein eL20
Bk: C2H2-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,466,83578
Polymers2,465,98465
Non-polymers85013
Water26,7881487
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 A1B1B2

#1: RNA chain 16S rRNA


Mass: 489213.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: GenBank: 18980902
#27: RNA chain 23S rRNA


Mass: 997978.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea)
#28: RNA chain 5S rRNA


Mass: 40589.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea)

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Small ribosomal subunit protein ... , 25 types, 25 molecules AaAbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAxBh

#2: Protein Small ribosomal subunit protein uS2 / 30S ribosomal protein S2


Mass: 23039.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0F0
#3: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 23464.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U004
#4: Protein Small ribosomal subunit protein eS1 / 30S ribosomal protein S3Ae / Ribosomal protein S1e


Mass: 22984.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZE1
#5: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P61993
#6: Protein Small ribosomal subunit protein eS4 / 30S ribosomal protein S4e


Mass: 28197.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U011
#7: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5 / PfS5


Mass: 26590.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U017
#8: Protein Small ribosomal subunit protein eS6 / 30S ribosomal protein S6e


Mass: 14002.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3H8
#9: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 24701.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0M8
#10: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14684.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U014
#11: Protein Small ribosomal subunit protein eS8 / 30S ribosomal protein S8e


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U1Y5
#12: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 15317.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E7
#13: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 11769.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P61885
#14: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 14756.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E3
#15: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P61995
#16: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 16948.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E2
#17: Protein Small ribosomal subunit protein uS14 / 30S ribosomal protein S14 type Z


Mass: 6634.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U013
#18: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 18640.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZD9
#19: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 13296.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U008
#20: Protein Small ribosomal subunit protein eS17 / 30S ribosomal protein S17e


Mass: 7942.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0U1
#21: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 15357.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U002
#22: Protein Small ribosomal subunit protein eS19


Mass: 17394.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0T4
#23: Protein Small ribosomal subunit protein eS24 / 30S ribosomal protein S24e


Mass: 11698.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U442
#24: Protein Small ribosomal subunit protein eS27 / 30S ribosomal protein S27e


Mass: 6888.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U474
#25: Protein Small ribosomal subunit protein eS28 / 30S ribosomal protein S28e


Mass: 8116.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U159
#60: 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 furiosus (archaea) / References: UniProt: Q8U232

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Protein , 2 types, 2 molecules AyBk

#26: Protein Zn-ribbon RNA-binding protein


Mass: 6824.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: I6U991
#63: Protein C2H2-type domain-containing protein


Mass: 7597.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U2K5

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Large ribosomal subunit protein ... , 33 types, 35 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBd...

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


Mass: 26085.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U001
#30: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 41465.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZZ8
#31: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 28765.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZZ9
#32: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 21269.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U012
#33: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 20891.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U015
#34: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13414.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U160
#35: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L10e


Mass: 20974.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q9UWP5
#36: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 16345.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E6
#37: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 15264.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U009
#38: Protein Large ribosomal subunit protein eL14 / 50S ribosomal protein L14e


Mass: 8979.659 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U2L5
#39: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 16439.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U018
#40: Protein Large ribosomal subunit protein eL15 / 50S ribosomal protein L15e


Mass: 22644.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U2F9
#41: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18 / PfL18


Mass: 23233.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q9HH80
#42: Protein Large ribosomal subunit protein eL18 / 50S ribosomal protein L18e


Mass: 13758.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0E5
#43: Protein Large ribosomal subunit protein eL19 / 50S ribosomal protein L19e / PfeL19


Mass: 17920.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U016
#44: Protein Large ribosomal subunit protein eL21 / 50S ribosomal protein L21e


Mass: 11371.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U217
#45: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 17679.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U003
#46: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 9893.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U000
#47: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 14364.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U010
#48: Protein Large ribosomal subunit protein eL24 / 50S ribosomal protein L24e


Mass: 7938.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U158
#49: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 8549.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U005
#50: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30 / PfL30


Mass: 17745.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q9HH78
#51: Protein Large ribosomal subunit protein eL30 / 50S ribosomal protein L30e


Mass: 10727.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0M6
#52: Protein Large ribosomal subunit protein eL31 / 50S ribosomal protein L31e


Mass: 11083.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3S7
#53: Protein Large ribosomal subunit protein eL32 / 50S ribosomal protein L32e / PfeL32


Mass: 15576.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q9HH82
#54: Protein Large ribosomal subunit protein eL34 / 50S ribosomal protein L34e


Mass: 10677.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U2L3
#55: Protein Large ribosomal subunit protein eL33 / 50S ribosomal protein L35Ae


Mass: 9755.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZV6
#56: Protein Large ribosomal subunit protein eL37 / 50S ribosomal protein L37e


Mass: 7245.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0P5
#57: Protein Large ribosomal subunit protein eL43 / 50S ribosomal protein L37Ae / Ribosomal protein L43e


Mass: 8956.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8TZI4
#58: Protein Large ribosomal subunit protein eL39 / 50S ribosomal protein L39e


Mass: 6323.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3S6
#59: Protein Large ribosomal subunit protein eL40 / 50S ribosomal protein L40e


Mass: 5858.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U0V6
#61: Protein Large ribosomal subunit protein eL42 / 50S ribosomal protein L44e


Mass: 11234.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U475
#62: Protein Large ribosomal subunit protein eL20 / 50S ribosomal protein L18Ae / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 9350.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q8U3S9

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Non-polymers , 2 types, 1500 molecules

#64: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: Zn
#65: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: P. furiosus 70S / Type: RIBOSOME / Entity ID: #1-#63 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Pyrococcus furiosus (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: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1.01 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37459 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002175654
ELECTRON MICROSCOPYf_angle_d0.534259653
ELECTRON MICROSCOPYf_dihedral_angle_d13.7961658
ELECTRON MICROSCOPYf_chiral_restr0.04331907
ELECTRON MICROSCOPYf_plane_restr0.00415822

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