8UU9 image
Deposition Date 2023-10-31
Release Date 2024-02-28
Last Version Date 2024-05-08
Entry Detail
PDB ID:
8UU9
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the ratcheted Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-D)
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Listeria monocytogenes EGD-e (Taxon ID: 169963)
Escherichia phage T4 (Taxon ID: 2681598)
Listeria innocua (Taxon ID: 1642)
Expression System(s):
Escherichia coli hb101, Escherichia coli bl21(de3)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8UU9 validation report missing
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmC
Chain IDs:SA (auth: 1)
Chain Length:63
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AGL9 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmD
Chain IDs:TA (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSJ1 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpsU
Chain IDs:UA (auth: 3)
Chain Length:81
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4MT39 Pfam ID:PF01197
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:VA (auth: 4)
Chain Length:57
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JNN0 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG
Chain IDs:WA (auth: 5)
Chain Length:49
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JRA4 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmH
Chain IDs:XA (auth: 6)
Chain Length:44
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JKZ6 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmI
Chain IDs:YA (auth: 7)
Chain Length:66
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JIB9 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmJ
Chain IDs:ZA (auth: 8)
Chain Length:37
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AM58 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:X (auth: A)
Chain Length:1550
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:Y (auth: B)
Chain Length:249
Number of Molecules:1
Biological Source:Listeria innocua
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:Z (auth: C)
Chain Length:277
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5A742 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplC
Chain IDs:AA (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5ADD0 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:BA (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSH7 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplE
Chain IDs:CA (auth: F)
Chain Length:97
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AWX6 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplF
Chain IDs:DA (auth: G)
Chain Length:178
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5ALU0 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:EA (auth: L)
Chain Length:137
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AGN0 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplN
Chain IDs:FA (auth: M)
Chain Length:121
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AP82 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:GA (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5A6S7 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:HA (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSU8 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:IA (auth: P)
Chain Length:135
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSW3 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplR
Chain IDs:JA (auth: Q)
Chain Length:119
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AR65 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplS
Chain IDs:KA (auth: R)
Chain Length:79
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A6B0JQF2 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplT
Chain IDs:LA (auth: S)
Chain Length:119
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JH71 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:MA (auth: T)
Chain Length:84
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AD18 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:NA (auth: U)
Chain Length:118
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5ANW2 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplW
Chain IDs:OA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4MTC5 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplX
Chain IDs:PA (auth: W)
Chain Length:103
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AD05 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:QA (auth: Y)
Chain Length:96
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JMC7 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmB
Chain IDs:RA (auth: Z)
Chain Length:62
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JJV9 Pfam ID:PF00830
Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A (auth: a)
Chain Length:1550
Number of Molecules:1
Biological Source:Listeria innocua
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsB
Chain IDs:B (auth: b)
Chain Length:249
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:Q92B01 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsC
Chain IDs:C (auth: c)
Chain Length:277
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSU9 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsD
Chain IDs:D (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:Q92BB2 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsE
Chain IDs:E (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSJ3 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsF
Chain IDs:F (auth: f)
Chain Length:97
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A7X0WKH5 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsG
Chain IDs:G (auth: g)
Chain Length:178
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JPE1 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsH
Chain IDs:H (auth: h)
Chain Length:132
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5A6U3 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsI
Chain IDs:I (auth: i)
Chain Length:130
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5ADS9 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsJ
Chain IDs:J (auth: j)
Chain Length:102
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5A730 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsK
Chain IDs:K (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AP31 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsL
Chain IDs:L (auth: l)
Chain Length:137
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JM56 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsM
Chain IDs:M (auth: m)
Chain Length:121
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5ARJ0 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsN
Chain IDs:N (auth: n)
Chain Length:61
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5AGZ1 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsO
Chain IDs:O (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JLK4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsP
Chain IDs:P (auth: p)
Chain Length:135
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A6B0JQE1 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: q)
Chain Length:119
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U5ADR4 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsR
Chain IDs:R (auth: r)
Chain Length:79
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JK14 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsS
Chain IDs:S (auth: s)
Chain Length:119
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A0U4VSH5 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsT
Chain IDs:T (auth: t)
Chain Length:84
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JML5 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTPase HflX
Gene (Uniprot):hflX
Chain IDs:W (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Listeria monocytogenes EGD-e
UniProt ID:Q8Y8Y0 Pfam ID:PF13167, PF16360, PF01926
Polymer Type:polyribonucleotide
Molecule:F-Stop mRNA
Chain IDs:V (auth: w)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia phage T4
Polymer Type:polyribonucleotide
Molecule:pe/E Hybrid State Phenylalani
Chain IDs:U (auth: x)
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
Ligand Molecules
GCP
MG
ZN
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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Protein

Chemical

Disease

Primary Citation of related structures
8UU9
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