8UU7 image
Entry Detail
PDB ID:
8UU7
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
Biological Source:
PDB Version:
Deposition Date:
2023-10-31
Release Date:
2024-02-28
Method Details:
Experimental Method:
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL29
Chain IDs:SA (auth: 1)
Chain Length:63
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL30
Chain IDs:TA (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL31B
Chain IDs:UA (auth: 3)
Chain Length:81
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL32
Chain IDs:VA (auth: 4)
Chain Length:57
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL33
Chain IDs:WA (auth: 5)
Chain Length:49
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL34
Chain IDs:XA (auth: 6)
Chain Length:44
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL35
Chain IDs:YA (auth: 7)
Chain Length:66
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL36
Chain IDs:ZA (auth: 8)
Chain Length:37
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polyribonucleotide
Description:23S Ribosomal RNA
Chain IDs:X (auth: A)
Chain Length:2932
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polyribonucleotide
Description:5S Ribosomal RNA
Chain IDs:Y (auth: B)
Chain Length:249
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL2
Chain IDs:Z (auth: C)
Chain Length:277
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL3
Chain IDs:AA (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL4
Chain IDs:BA (auth: E)
Chain Length:207
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL5
Chain IDs:CA (auth: F)
Chain Length:97
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL6
Chain IDs:DA (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL13
Chain IDs:EA (auth: L)
Chain Length:145
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL14
Chain IDs:FA (auth: M)
Chain Length:122
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL15
Chain IDs:GA (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL16
Chain IDs:HA (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL17
Chain IDs:IA (auth: P)
Chain Length:90
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL18
Chain IDs:JA (auth: Q)
Chain Length:87
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL19
Chain IDs:KA (auth: R)
Chain Length:114
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL20
Chain IDs:LA (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL21
Chain IDs:MA (auth: T)
Chain Length:84
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL22
Chain IDs:NA (auth: U)
Chain Length:118
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL23
Chain IDs:OA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL24
Chain IDs:PA (auth: W)
Chain Length:103
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL27
Chain IDs:QA (auth: Y)
Chain Length:76
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL28
Chain IDs:RA (auth: Z)
Chain Length:62
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polyribonucleotide
Description:16S Ribosomal RNA
Chain IDs:A (auth: a)
Chain Length:2932
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS2
Chain IDs:B (auth: b)
Chain Length:249
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS3
Chain IDs:C (auth: c)
Chain Length:277
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS4
Chain IDs:D (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS5
Chain IDs:E (auth: e)
Chain Length:207
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS6
Chain IDs:F (auth: f)
Chain Length:97
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS7
Chain IDs:G (auth: g)
Chain Length:156
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS8
Chain IDs:H (auth: h)
Chain Length:132
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS9
Chain IDs:I (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS10
Chain IDs:J (auth: j)
Chain Length:102
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS11
Chain IDs:K (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS12
Chain IDs:L (auth: l)
Chain Length:145
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS13
Chain IDs:M (auth: m)
Chain Length:122
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS14
Chain IDs:N (auth: n)
Chain Length:61
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS15
Chain IDs:O (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS16
Chain IDs:P (auth: p)
Chain Length:90
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS17
Chain IDs:Q (auth: q)
Chain Length:87
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS18
Chain IDs:R (auth: r)
Chain Length:114
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS19
Chain IDs:S (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS20
Chain IDs:T (auth: t)
Chain Length:84
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Description:GTPase HflX
Chain IDs:V (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Listeria monocytogenes EGD-e
Polymer Type:polypeptide(L)
Description:Ribosome hibernation promoting factor
Chain IDs:W (auth: w)
Chain Length:103
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polyribonucleotide
Description:E-site Phenylalanine tRNA
Chain IDs:U (auth: y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU U U modified residue
5MU U U modified residue
7MG U G modified residue
MIA U A modified residue
PSU U U modified residue
Primary Citation
Mechanistic insights into the alternative ribosome recycling by HflXr.
Nucleic Acids Res. 52 4053 4066 (2024)
PMID: 38407413 DOI: 10.1093/nar/gkae128

Abstact

During stress conditions such as heat shock and antibiotic exposure, ribosomes stall on messenger RNAs, leading to inhibition of protein synthesis. To remobilize ribosomes, bacteria use rescue factors such as HflXr, a homolog of the conserved housekeeping GTPase HflX that catalyzes the dissociation of translationally inactive ribosomes into individual subunits. Here we use time-resolved cryo-electron microscopy to elucidate the mechanism of ribosome recycling by Listeria monocytogenes HflXr. Within the 70S ribosome, HflXr displaces helix H69 of the 50S subunit and induces long-range movements of the platform domain of the 30S subunit, disrupting inter-subunit bridges B2b, B2c, B4, B7a and B7b. Our findings unveil a unique ribosome recycling strategy by HflXr which is distinct from that mediated by RRF and EF-G. The resemblance between HflXr and housekeeping HflX suggests that the alternative ribosome recycling mechanism reported here is universal in the prokaryotic kingdom.

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Primary Citation of related structures