6GZQ image
Entry Detail
PDB ID:
6GZQ
EMDB ID:
Keywords:
Title:
T. thermophilus hibernating 70S ribosome
Biological Source:
PDB Version:
Deposition Date:
2018-07-04
Release Date:
2018-10-24
Method Details:
Experimental Method:
Resolution:
3.28 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:CA (auth: A1)
Chain Length:2912
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:AB (auth: A2)
Chain Length:1506
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:DA (auth: B1)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:FA (auth: B2)
Chain Length:237
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:A (auth: C1)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:GA (auth: C2)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:B (auth: D1)
Chain Length:205
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:HA (auth: D2)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus HB8
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:C (auth: E1)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:IA (auth: E2)
Chain Length:151
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:D (auth: F1)
Chain Length:181
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:JA (auth: F2)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:E (auth: G1)
Chain Length:170
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:KA (auth: G2)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:F (auth: H1)
Chain Length:50
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:LA (auth: H2)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:G (auth: I1)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:MA (auth: I2)
Chain Length:127
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:H (auth: J1)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:NA (auth: J2)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:I (auth: K1)
Chain Length:150
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:OA (auth: K2)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:J (auth: L1)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:PA (auth: L2)
Chain Length:125
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:K (auth: M1)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:QA (auth: M2)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:L (auth: N1)
Chain Length:111
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14 type Z
Chain IDs:RA (auth: N2)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:M (auth: O1)
Chain Length:137
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:SA (auth: O2)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:N (auth: P1)
Chain Length:117
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:TA (auth: P2)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:O (auth: Q1)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:UA (auth: Q2)
Chain Length:100
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:P (auth: R1)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:VA (auth: R2)
Chain Length:62
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:Q (auth: S1)
Chain Length:92
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:WA (auth: S2)
Chain Length:78
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:R (auth: T1)
Chain Length:102
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:XA (auth: T2)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:S (auth: U1)
Chain Length:179
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:30S ribosomal protein Thx
Chain IDs:YA (auth: U2)
Chain Length:25
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:T (auth: V1)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:Ribosome hibernation promoting factor
Chain IDs:ZA (auth: V2)
Chain Length:121
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:U (auth: W1)
Chain Length:97
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:V (auth: X1)
Chain Length:69
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:W (auth: Y1)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:X (auth: Z1)
Chain Length:63
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:Y (auth: a1)
Chain Length:2912
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:Z (auth: b1)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:AA (auth: c1)
Chain Length:49
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:BA (auth: d1)
Chain Length:205
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:EA (auth: e1)
Chain Length:208
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Ligand Molecules
Primary Citation
Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
Nat Commun 9 4179 4179 (2018)
PMID: 30301898 DOI: 10.1038/s41467-018-06724-x

Abstact

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.

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Primary Citation of related structures