4V6U

Promiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Promiscuous behaviour of archaeal ribosomal proteins: Implications for eukaryotic ribosome evolution.

Armache, J.P.Anger, A.M.Marquez, V.Franckenberg, S.Frohlich, T.Villa, E.Berninghausen, O.Thomm, M.Arnold, G.J.Beckmann, R.Wilson, D.N.

(2013) Nucleic Acids Res 41: 1284-1293

  • DOI: 10.1093/nar/gks1259
  • Primary Citation of Related Structures:  
    4V6U

  • PubMed 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, only molecular models of large 50S subunits have been reported for archaea ...

    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.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15P/S13eA [auth AQ]158Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps15PF2056
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Entity ID: 2
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30S ribosomal protein S9PB [auth AK]135Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps9PF1644
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Find proteins for Q8U0E7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 3
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30S ribosomal protein S8PC [auth AI]130Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps8PF1809
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Entity ID: 4
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30S ribosomal protein S6eD [auth AG]125Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps6ePF0488
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Find proteins for Q8U3H8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 5
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30S ribosomal protein S27eE [auth AW]63Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps27ePF0218
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Entity ID: 6
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30S ribosomal protein S3PF [auth AC]210Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps3PF1819
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Entity ID: 7
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30S ribosomal protein S2PG [auth AB]202Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps2PF1640
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Find proteins for Q8U0F0 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 8
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30S ribosomal protein S17PH [auth AR]113Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps17PF1815
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Entity ID: 9
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unknown 30S ribosomal protein SXI [auth A9]57Pyrococcus furiosus DSM 3638Mutation(s): 0 
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Entity ID: 10
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30S ribosomal protein S4PJ [auth AD]180Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps4PF1649
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Find proteins for P61993 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 12
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30S ribosomal protein S12PL [auth AN]147Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps12PF1559
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Entity ID: 13
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30S ribosomal protein S28eM [auth AX]71Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps28ePF1368
UniProt
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Entity ID: 14
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30S ribosomal protein S11PN [auth AM]137Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps11PF1648
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Find proteins for Q8U0E3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 15
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30S ribosomal protein S4eO [auth AE]243Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps4ePF1812
UniProt
Find proteins for Q8U011 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 16
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30S ribosomal protein S8eP [auth AJ]127Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps8ePF1069
UniProt
Find proteins for Q8U1Y5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 17
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30S ribosomal protein S13PQ [auth AO]148Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps13PF1650
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Find proteins for Q8U0E2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 18
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30S ribosomal protein S5PR [auth AF]236Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps5PF1804
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Find proteins for Q8U017 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 19
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30S ribosomal protein S17eS [auth AS]67Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps17ePF1491
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Find proteins for Q8U0U1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7AeT [auth A3],
OB [auth B4],
BB [auth BG]
123Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl7aePF1367
UniProt
Find proteins for Q8U160 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 22
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30S ribosomal protein S27aeV [auth AY]50Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps27aePF0252
UniProt
Find proteins for Q8U443 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 23
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30S ribosomal protein S19PW [auth AT]132Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps19PF1821
UniProt
Find proteins for Q8U002 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AeX [auth AA]198Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps3aePF2054
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Find proteins for Q8TZE1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 25
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30S ribosomal protein S7PY [auth AH]215Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps7PF1558
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Entity ID: 26
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30S ribosomal protein S14P type ZZ [auth AP]56Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps14PF1810
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Entity ID: 28
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30S ribosomal protein S24eBA [auth AV],
HB [auth B6]
99Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps24ePF0253
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Entity ID: 29
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30S ribosomal protein S10PCA [auth AL]102Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps10PF1376
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Entity ID: 30
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SSU ribosomal protein S19EDA [auth AU]150Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rps19ePF1499
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Entity ID: 31
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50S ribosomal protein L30PEA [auth BY]155Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl30PF1803
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Entity ID: 32
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50S ribosomal protein L18PFA [auth BO]203Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl18PF1805
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Entity ID: 33
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50S ribosomal protein L3PGA [auth BC]365Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl3PF1825
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Entity ID: 34
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50S ribosomal protein L14eHA [auth B5],
WA [auth BK]
83Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl14ePF0819
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Entity ID: 35
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50S ribosomal protein L15PIA [auth BL]147Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl15PF1802
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Entity ID: 36
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50S ribosomal protein L39eJA [auth Bf]51Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl39ePF0379
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Find proteins for Q8U3S6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 37
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50S ribosomal protein L24PKA [auth BU]121Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl24PF1813
UniProt
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Entity ID: 38
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50S ribosomal protein L32eLA [auth Bb]130Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl32ePF1807
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Entity ID: 39
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50S ribosomal protein L37eMA [auth Be]62Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl37ePF1541
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Entity ID: 40
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50S ribosomal protein L5PNA [auth BE]186Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl5PF1811
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Find proteins for Q8U012 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 41
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50S ribosomal protein L31eOA [auth Ba]95Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl31ePF0378
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Find proteins for Q8U3S7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PPA [auth BT]86Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl23PF1823
UniProt
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Entity ID: 43
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Acidic ribosomal protein P0 homologQA [auth Bk]339Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl10rplP0PF1993
UniProt
Find proteins for Q8TZJ8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 44
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50S ribosomal protein L29PRA [auth BW]72Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl29PF1818
UniProt
Find proteins for Q8U005 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 45
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50S ribosomal protein L37AeSA [auth Bi]83Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl37aePF2008
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Entity ID: 46
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50S ribosomal protein L1PTA [auth BA]216Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl1PF1992
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Entity ID: 47
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50S ribosomal protein L13PUA [auth BI]142Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl13PF1645
UniProt
Find proteins for Q8U0E6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 48
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50S ribosomal protein L21eVA [auth BR]97Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl21ePF1035
UniProt
Find proteins for Q8U217 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 49
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50S ribosomal protein L19eXA [auth BQ]150Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl19ePF1806
UniProt
Find proteins for Q8U016 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 50
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50S ribosomal protein L24eYA [auth BV]66Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl24ePF1369
UniProt
Find proteins for Q8U158 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 51
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50S ribosomal protein L44EZA [auth Bj]94Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl44ePF0217
UniProt
Find proteins for Q8U475 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 52
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50S ribosomal protein L2PAB [auth BB]239Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl2PF1822
UniProt
Find proteins for Q8U001 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 53
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50S ribosomal protein L4PCB [auth BD]255Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl4PF1824
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Entity ID: 54
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50S ribosomal protein L6PDB [auth BF]184Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl6PF1808
UniProt
Find proteins for Q8U015 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 55
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50S ribosomal protein L41eEB [auth Bh]24Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl41ePF1018
UniProt
Find proteins for Q8U232 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 56
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50S ribosomal protein L11PFB [auth BH]164Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl11PF1991
UniProt
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Entity ID: 57
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50S ribosomal protein L30eGB [auth BZ]99Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl30ePF1561
UniProt
Find proteins for Q8U0M6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 58
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50S ribosomal protein L18eIB [auth BP]120Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl18ePF1646
UniProt
Find proteins for Q8U0E5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 59
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50S ribosomal protein L15eJB [auth BM]194Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl15ePF0876
UniProt
Find proteins for Q8U2F9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 60
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50S ribosomal protein L22PKB [auth BS]155Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl22PF1820
UniProt
Find proteins for Q8U003 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 61
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50S ribosomal protein L34eLB [auth Bd]89Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl34ePF0821
UniProt
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Entity ID: 62
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50S ribosomal protein L10eMB [auth BN]181Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl10ePF1279
UniProt
Find proteins for Q9UWP5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 63
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50S ribosomal protein L40eNB [auth Bg]51Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl40ePF1475
UniProt
Find proteins for Q8U0V6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 64
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50S ribosomal protein L35AePB [auth Bc]87Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl35aePF1872
UniProt
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Entity ID: 65
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50S ribosomal protein L14PQB [auth BJ]141Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl14PF1814
UniProt
Find proteins for Q8U009 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Entity ID: 66
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50S ribosomal protein LXRB [auth Bl]77Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: rpl18arpl20erplXPF0376
UniProt
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Entity ID: 11
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E-tRNAK [auth A1]77Pyrococcus furiosus DSM 3638
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Entity ID: 21
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16S rRNAU [auth A2]1,495Pyrococcus furiosus DSM 3638
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Entity ID: 27
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P-tRNAAA [auth A0]76Pyrococcus furiosus DSM 3638
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Entity ID: 67
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23S rRNASB [auth B1]3,049Pyrococcus furiosus DSM 3638
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Entity ID: 68
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5S rRNATB [auth B3]126Pyrococcus furiosus DSM 3638
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-01
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Other