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- PDB-4v6u: Promiscuous behavior of proteins in archaeal ribosomes revealed b... -

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Basic information

Entry
Database: PDB / ID: 4v6u
TitlePromiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes
Components
  • (30S ribosomal protein ...) x 24
  • (50S ribosomal protein ...) x 36
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • Acidic ribosomal protein P0 homolog
  • E-tRNA
  • P-tRNA
  • SSU ribosomal protein S19E
  • unknown 30S ribosomal protein SX
KeywordsRIBOSOME / archaea / archaeal / ribosomal / 70S / kink-turn / protein synthesis / RNA
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 / regulation of translation / large ribosomal subunit / 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 / rRNA processing / regulation of translation / 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 L1, archaea / Ribosomal protein L14e / : / Ribosomal protein L14, KOW motif / Ribosomal protein L40e, archaeal / Ribosomal protein S27ae / 50S ribosomal protein L10, archaea / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal ...Ribosomal protein L1, archaea / Ribosomal protein L14e / : / Ribosomal protein L14, KOW motif / Ribosomal protein L40e, archaeal / Ribosomal protein S27ae / 50S ribosomal protein L10, archaea / 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 / 60s Acidic ribosomal protein / : / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L23 / : / Ribosomal protein L2, archaeal-type / metallochaperone-like domain / TRASH domain / Ribosomal protein L1, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L1 / 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 L1, 3-layer alpha/beta-sandwich / 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 S27a / Ribosomal protein S27a / Ribosomal protein S27a / 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 L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein S27e signature.
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 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 uL10 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / 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 / 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 eS31 / 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: 6.6 Å
AuthorsArmache, J.-P. / Anger, A.M. / Marquez, V. / Frankenberg, S. / Froehlich, T. / Villa, E. / Berninghausen, O. / Thomm, M. / Arnold, G.J. / Beckmann, R. / Wilson, D.N.
CitationJournal: Nucleic Acids Res / Year: 2013
Title: Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution.
Authors: Jean-Paul Armache / Andreas M Anger / Viter Márquez / Sibylle Franckenberg / Thomas Fröhlich / Elizabeth Villa / Otto Berninghausen / Michael Thomm / Georg J Arnold / Roland Beckmann / Daniel N Wilson /
Abstract: In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, ...In all living cells, protein synthesis occurs on ribonucleoprotein particles called ribosomes. Molecular models have been reported for complete bacterial 70S and eukaryotic 80S ribosomes; however, only molecular models of large 50S subunits have been reported for archaea. Here, we present a complete molecular model for the Pyrococcus furiosus 70S ribosome based on a 6.6 Å cryo-electron microscopy map. Moreover, we have determined cryo-electron microscopy reconstructions of the Euryarchaeota Methanococcus igneus and Thermococcus kodakaraensis 70S ribosomes and Crenarchaeota Staphylothermus marinus 50S subunit. Examination of these structures reveals a surprising promiscuous behavior of archaeal ribosomal proteins: We observe intersubunit promiscuity of S24e and L8e (L7ae), the latter binding to the head of the small subunit, analogous to S12e in eukaryotes. Moreover, L8e and L14e exhibit intrasubunit promiscuity, being present in two copies per archaeal 50S subunit, with the additional binding site of L14e analogous to the related eukaryotic r-protein L27e. Collectively, these findings suggest insights into the evolution of eukaryotic ribosomal proteins through increased copy number and binding site promiscuity.
History
DepositionAug 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J20, 3J21, 3J2L
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 1, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5Feb 1, 2023Group: Database references / Category: citation_author / database_2
Item: _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6May 15, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
AQ: 30S ribosomal protein S15P/S13e
AK: 30S ribosomal protein S9P
AI: 30S ribosomal protein S8P
AG: 30S ribosomal protein S6e
AW: 30S ribosomal protein S27e
AC: 30S ribosomal protein S3P
AB: 30S ribosomal protein S2P
AR: 30S ribosomal protein S17P
A9: unknown 30S ribosomal protein SX
AD: 30S ribosomal protein S4P
A1: E-tRNA
AN: 30S ribosomal protein S12P
AX: 30S ribosomal protein S28e
AM: 30S ribosomal protein S11P
AE: 30S ribosomal protein S4e
AJ: 30S ribosomal protein S8e
AO: 30S ribosomal protein S13P
AF: 30S ribosomal protein S5P
AS: 30S ribosomal protein S17e
A3: 50S ribosomal protein L7Ae
A2: 16S rRNA
AY: 30S ribosomal protein S27ae
AT: 30S ribosomal protein S19P
AA: 30S ribosomal protein S3Ae
AH: 30S ribosomal protein S7P
AP: 30S ribosomal protein S14P type Z
A0: P-tRNA
AV: 30S ribosomal protein S24e
AL: 30S ribosomal protein S10P
AU: SSU ribosomal protein S19E
BY: 50S ribosomal protein L30P
BO: 50S ribosomal protein L18P
BC: 50S ribosomal protein L3P
B5: 50S ribosomal protein L14e
BL: 50S ribosomal protein L15P
Bf: 50S ribosomal protein L39e
BU: 50S ribosomal protein L24P
Bb: 50S ribosomal protein L32e
Be: 50S ribosomal protein L37e
BE: 50S ribosomal protein L5P
Ba: 50S ribosomal protein L31e
BT: 50S ribosomal protein L23P
Bk: Acidic ribosomal protein P0 homolog
BW: 50S ribosomal protein L29P
Bi: 50S ribosomal protein L37Ae
BA: 50S ribosomal protein L1P
BI: 50S ribosomal protein L13P
BR: 50S ribosomal protein L21e
BK: 50S ribosomal protein L14e
BQ: 50S ribosomal protein L19e
BV: 50S ribosomal protein L24e
Bj: 50S ribosomal protein L44E
BB: 50S ribosomal protein L2P
BG: 50S ribosomal protein L7Ae
BD: 50S ribosomal protein L4P
BF: 50S ribosomal protein L6P
Bh: 50S ribosomal protein L41e
BH: 50S ribosomal protein L11P
BZ: 50S ribosomal protein L30e
B6: 30S ribosomal protein S24e
BP: 50S ribosomal protein L18e
BM: 50S ribosomal protein L15e
BS: 50S ribosomal protein L22P
Bd: 50S ribosomal protein L34e
BN: 50S ribosomal protein L10e
Bg: 50S ribosomal protein L40e
B4: 50S ribosomal protein L7Ae
Bc: 50S ribosomal protein L35Ae
BJ: 50S ribosomal protein L14P
Bl: 50S ribosomal protein LX
B1: 23S rRNA
B3: 5S rRNA


Theoretical massNumber of molelcules
Total (without water)2,602,98572
Polymers2,602,98572
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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30S ribosomal protein ... , 24 types, 25 molecules AQAKAIAGAWACABARADANAXAMAEAJAOAFASAYATAAAHAPAVB6AL

#1: Protein 30S ribosomal protein S15P/S13e / 30S ribosomal protein S15


Mass: 18640.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZD9
#2: Protein 30S ribosomal protein S9P / 30S ribosomal protein S9


Mass: 15317.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0E7
#3: Protein 30S ribosomal protein S8P / 30S ribosomal protein S8


Mass: 14684.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U014
#4: Protein 30S ribosomal protein S6e


Mass: 14002.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U3H8
#5: Protein 30S ribosomal protein S27e


Mass: 6888.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U474
#6: Protein 30S ribosomal protein S3P / 30S ribosomal protein S3


Mass: 23464.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U004
#7: Protein 30S ribosomal protein S2P / 30S ribosomal protein S2


Mass: 23039.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0F0
#8: Protein 30S ribosomal protein S17P / 30S ribosomal protein S17


Mass: 13296.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U008
#10: Protein 30S ribosomal protein S4P / 30S ribosomal protein S4


Mass: 21381.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: P61993
#12: Protein 30S ribosomal protein S12P / 30S ribosomal protein S12


Mass: 16477.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: P61995
#13: Protein 30S ribosomal protein S28e


Mass: 8116.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U159
#14: Protein 30S ribosomal protein S11P / 30S ribosomal protein S11


Mass: 14756.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0E3
#15: Protein 30S ribosomal protein S4e


Mass: 28197.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U011
#16: Protein 30S ribosomal protein S8e


Mass: 14293.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U1Y5
#17: Protein 30S ribosomal protein S13P / 30S ribosomal protein S13


Mass: 16948.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0E2
#18: Protein 30S ribosomal protein S5P / PfS5 / 30S ribosomal protein S5


Mass: 26590.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U017
#19: Protein 30S ribosomal protein S17e


Mass: 7942.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0U1
#22: Protein/peptide 30S ribosomal protein S27ae / 30S ribosomal protein S31e


Mass: 5864.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U443
#23: Protein 30S ribosomal protein S19P / 30S ribosomal protein S19


Mass: 15357.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U002
#24: Protein 30S ribosomal protein S3Ae / 30S ribosomal protein S1e


Mass: 22984.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZE1
#25: Protein 30S ribosomal protein S7P / 30S ribosomal protein S7


Mass: 24701.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0M8
#26: Protein 30S ribosomal protein S14P type Z / 30S ribosomal protein S14


Mass: 6634.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U013
#28: Protein 30S ribosomal protein S24e


Mass: 11698.564 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U442
#29: Protein 30S ribosomal protein S10P / 30S ribosomal protein S10


Mass: 11769.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: P61885

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Protein , 3 types, 3 molecules A9AUBk

#9: Protein unknown 30S ribosomal protein SX


Mass: 4868.993 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
#30: Protein SSU ribosomal protein S19E / 30S ribosomal protein S19e


Mass: 17394.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0T4
#43: Protein Acidic ribosomal protein P0 homolog / L10E / 50S ribosomal protein P0


Mass: 37166.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZJ8

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RNA chain , 5 types, 5 molecules A1A2A0B1B3

#11: RNA chain E-tRNA


Mass: 24880.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
#21: RNA chain 16S rRNA


Mass: 485455.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
#27: RNA chain P-tRNA


Mass: 24538.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
#67: RNA chain 23S rRNA


Mass: 990820.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
#68: RNA chain 5S rRNA


Mass: 40689.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1

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50S ribosomal protein ... , 36 types, 39 molecules A3BGB4BYBOBCB5BKBLBfBUBbBeBEBaBTBWBiBABIBRBQBVBjBBBDBFBhBHBZ...

#20: Protein 50S ribosomal protein L7Ae / 30S ribosomal protein L8e(S)


Mass: 13414.664 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U160
#31: Protein 50S ribosomal protein L30P / PfL30 / 50S ribosomal protein L30


Mass: 17745.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q9HH78
#32: Protein 50S ribosomal protein L18P / PfL18 / 50S ribosomal protein L18


Mass: 23233.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q9HH80
#33: Protein 50S ribosomal protein L3P / 50S ribosomal protein L3


Mass: 41465.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZZ8
#34: Protein 50S ribosomal protein L14e


Mass: 8979.659 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U2L5
#35: Protein 50S ribosomal protein L15P / 50S ribosomal protein L15


Mass: 16439.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U018
#36: Protein 50S ribosomal protein L39e


Mass: 6323.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U3S6
#37: Protein 50S ribosomal protein L24P / 50S ribosomal protein L24


Mass: 14364.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U010
#38: Protein 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) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q9HH82
#39: Protein 50S ribosomal protein L37e


Mass: 7245.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0P5
#40: Protein 50S ribosomal protein L5P / 50S ribosomal protein L5


Mass: 21269.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U012
#41: Protein 50S ribosomal protein L31e


Mass: 11083.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U3S7
#42: Protein 50S ribosomal protein L23P / 50S ribosomal protein L23


Mass: 9893.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U000
#44: Protein 50S ribosomal protein L29P / 50S ribosomal protein L29


Mass: 8549.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U005
#45: Protein 50S ribosomal protein L37Ae / 50S ribosomal protein L43e


Mass: 8956.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZI4
#46: Protein 50S ribosomal protein L1P / 50S ribosomal protein L1


Mass: 23893.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZJ9
#47: Protein 50S ribosomal protein L13P / 50S ribosomal protein L13


Mass: 16345.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0E6
#48: Protein 50S ribosomal protein L21e


Mass: 11371.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U217
#49: Protein 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) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U016
#50: Protein 50S ribosomal protein L24e


Mass: 7938.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U158
#51: Protein 50S ribosomal protein L44E


Mass: 11234.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U475
#52: Protein 50S ribosomal protein L2P / 50S ribosomal protein L2


Mass: 26085.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U001
#53: Protein 50S ribosomal protein L4P / 50S ribosomal protein L4


Mass: 28765.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZZ9
#54: Protein 50S ribosomal protein L6P / 50S ribosomal protein L6


Mass: 20891.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U015
#55: Protein/peptide 50S ribosomal protein L41e


Mass: 3277.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U232
#56: Protein 50S ribosomal protein L11P / 50S ribosomal protein L11


Mass: 17657.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZK0
#57: Protein 50S ribosomal protein L30e


Mass: 10727.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0M6
#58: Protein 50S ribosomal protein L18e


Mass: 13758.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0E5
#59: Protein 50S ribosomal protein L15e


Mass: 22644.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U2F9
#60: Protein 50S ribosomal protein L22P / 50S ribosomal protein L22


Mass: 17679.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U003
#61: Protein 50S ribosomal protein L34e


Mass: 10677.132 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U2L3
#62: Protein 50S ribosomal protein L10e / 50S ribosomal protein L16


Mass: 20974.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q9UWP5
#63: Protein 50S ribosomal protein L40e


Mass: 5858.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U0V6
#64: Protein 50S ribosomal protein L35Ae / 50S ribosomal protein L33e


Mass: 9755.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8TZV6
#65: Protein 50S ribosomal protein L14P / 50S ribosomal protein L14


Mass: 15264.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U009
#66: Protein 50S ribosomal protein LX


Mass: 9350.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U3S9

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Details

Sequence detailsTHE SEQUENCE OF 30S RIBOSOMAL PROTEIN SX IS NOT KNOWN.

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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: Pyrococcus furiosus 70S ribosome / Type: RIBOSOME
Buffer solutionName: 56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP
pH: 8.2
Details: 56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil grids (3/3) with 2 nm carbon on top
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 %
Details: Blot for 10 seconds before plunging into liquid ethane, using 2 layers of filter paper (FEI VITROBOT)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: Wiener Filter
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Single Particle / Resolution: 6.6 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 10000 / Nominal pixel size: 1.24 Å / Actual pixel size: 1.24 Å
Details: sorting for ribosome conformation and ligand presence was performed
Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms28609 35409 0 0 64018

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