6GZX

T. thermophilus hibernating 100S ribosome (ice)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.

Flygaard, R.K.Boegholm, N.Yusupov, M.Jenner, L.B.

(2018) Nat Commun 9: 4179-4179

  • DOI: 10.1038/s41467-018-06724-x
  • Primary Citation of Related Structures:  
    6GZZ, 6GZQ, 6GZX

  • PubMed Abstract: 
  • In response to cellular stresses bacteria conserve energy by dimerization of ribosomes into inactive hibernating 100S ribosome particles. Ribosome dimerization in Thermus thermophilus is facilitated by hibernation-promoting factor (TtHPF). In this study we demonstrate high sensitivity of Tt100S formation to the levels of TtHPF and show that a 1:1 ratio leads to optimal dimerization ...

    In response to cellular stresses bacteria conserve energy by dimerization of ribosomes into inactive hibernating 100S ribosome particles. Ribosome dimerization in Thermus thermophilus is facilitated by hibernation-promoting factor (TtHPF). In this study we demonstrate high sensitivity of Tt100S formation to the levels of TtHPF and show that a 1:1 ratio leads to optimal dimerization. We report structures of the T. thermophilus 100S ribosome determined by cryo-electron microscopy to average resolutions of 4.13 Å and 4.57 Å. In addition, we present a 3.28 Å high-resolution cryo-EM reconstruction of a 70S ribosome from a hibernating ribosome dimer and reveal a role for the linker region connecting the TtHPF N- and C-terminal domains in translation inhibition by preventing Shine-Dalgarno duplex formation. Our work demonstrates that species-specific differences in the dimerization interface govern the overall conformation of the 100S ribosome particle and that for Thermus thermophilus no ribosome-ribosome interactions are involved in the interface.


    Organizational Affiliation

    Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS UMR710, INSERM U964, University of Strasbourg, Strasbourg, 67000, France. lasse@igbmc.fr.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 C1C2272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3 D1D2205Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4 E1E2208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5 F1F2181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6 G1G2170Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9 H1H250Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13 I1I2138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14 J1J2122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15 K1K2150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 L1L2141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 M1M2117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 N1N2111Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 O1O2137Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 P1P2117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 Q1Q2101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22 R1R2113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 17
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50S ribosomal protein L23 S1S292Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24 T1T2102Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 U1U2179Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
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50S ribosomal protein L27 V1V277Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28 W1W297Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29 X1X269Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 Y1Y259Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31 Z1Z263Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 a1a259Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 b1b245Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 c1c249Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 d1d261Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 e1e236Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 B3B4237Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3 C3C4206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 D3D4208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 E3E4151Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6 F3F4101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 37
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30S ribosomal protein S7 G3G4155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8 H3H4138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 I3I4127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 J3J499Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 K3K4118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 L3L4125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 43
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30S ribosomal protein S13 M3M4117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z N3N460Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 O3O488Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16 P3P484Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 47
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30S ribosomal protein S17 Q3Q4100Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 48
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30S ribosomal protein S18 R3R462Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 49
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30S ribosomal protein S19 S3S478Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20 T3T499Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx U3U425Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promoting factor W4X357Thermus thermophilus HB8Mutation(s): 0 
Gene Names: hpfTTHA1294
Find proteins for Q5SIS0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promoting factor V3V4119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: hpfTTHA1294
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Entity ID: 29
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA1, A22912Thermus thermophilus HB8
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Entity ID: 30
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB1, B2122Thermus thermophilus HB8
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Entity ID: 53
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA3, A41506Thermus thermophilus HB8
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF12OC1015894

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release