6H4N image
Entry Detail
PDB ID:
6H4N
EMDB ID:
Keywords:
Title:
Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2018-07-22
Release Date:
2018-09-05
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:UA (auth: 0)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:VA (auth: 1)
Chain Length:50
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:WA (auth: 2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:XA (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:YA (auth: 4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:ZA (auth: 6)
Chain Length:66
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:V (auth: A)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:W (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:X (auth: C)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:Y (auth: D)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:Z (auth: E)
Chain Length:157
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:AA (auth: F)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:BA (auth: G)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:CA (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:RNA (5'-R(P*CP*UP*CP*CP*U)-3')
Chain IDs:EB (auth: I)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:DA (auth: J)
Chain Length:98
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:EA (auth: K)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:FA (auth: L)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:GA (auth: M)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:HA (auth: N)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:IA (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:JA (auth: P)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:KA (auth: Q)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:LA (auth: R)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:MA (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:NA (auth: T)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:OA (auth: U)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:PA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:QA (auth: W)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:RA (auth: X)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:SA (auth: Y)
Chain Length:557
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:TA (auth: Z)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:A (auth: a)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:B (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:C (auth: c)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:D (auth: d)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:E (auth: e)
Chain Length:157
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:F (auth: f)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:G (auth: g)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:H (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:I (auth: i)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:J (auth: j)
Chain Length:98
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:K (auth: k)
Chain Length:116
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:L (auth: l)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:M (auth: m)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:N (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:O (auth: o)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:P (auth: p)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:Q (auth: q)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:R (auth: r)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:S (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:T (auth: t)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:U (auth: u)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:Ribosome modulation factor
Chain IDs:BB (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:tRNA
Chain IDs:AB (auth: w)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:Ribosome hibernation promoting factor
Chain IDs:DB (auth: x)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S1
Chain IDs:CB (auth: y)
Chain Length:557
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Ligand Molecules
Primary Citation
Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.
Nat Microbiol 3 1115 1121 (2018)
PMID: 30177741 DOI: 10.1038/s41564-018-0237-0

Abstact

To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles1. In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF)2-4. Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria5-8, and reveals a unique role for bS1 in translation regulation.

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Primary Citation of related structures