8UU7 image
Deposition Date 2023-10-31
Release Date 2024-02-28
Last Version Date 2024-05-08
Entry Detail
PDB ID:
8UU7
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the Listeria innocua 70S ribosome in complex with HflXr, HPF, and E-site tRNA (structure II-B)
Biological Source:
Source Organism:
Listeria innocua (Taxon ID: 1642)
Escherichia coli (Taxon ID: 562)
Listeria monocytogenes EGD-e (Taxon ID: 169963)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8UU7 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
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 protein uL30
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 protein bL31B
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 protein bL32
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 protein bL33
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 protein bL34
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 protein bL35
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 protein bL36
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:2932
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 protein uL2
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 protein uL3
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 protein uL4
Gene (Uniprot):rplD
Chain IDs:BA (auth: E)
Chain Length:207
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 protein uL5
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 protein uL6
Gene (Uniprot):rplF
Chain IDs:DA (auth: G)
Chain Length:156
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 protein uL13
Gene (Uniprot):rplM
Chain IDs:EA (auth: L)
Chain Length:145
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 protein uL14
Gene (Uniprot):rplN
Chain IDs:FA (auth: M)
Chain Length:122
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 protein uL15
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 protein uL16
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 protein bL17
Gene (Uniprot):rplQ
Chain IDs:IA (auth: P)
Chain Length:90
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 protein uL18
Gene (Uniprot):rplR
Chain IDs:JA (auth: Q)
Chain Length:87
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 protein bL19
Gene (Uniprot):rplS
Chain IDs:KA (auth: R)
Chain Length:114
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 protein bL20
Gene (Uniprot):rplT
Chain IDs:LA (auth: S)
Chain Length:92
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 protein bL21
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 protein uL22
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 protein uL23
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 protein uL24
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 protein bL27
Gene (Uniprot):rpmA
Chain IDs:QA (auth: Y)
Chain Length:76
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 protein bL28
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:2932
Number of Molecules:1
Biological Source:Listeria innocua
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Chain IDs:B (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:Small ribosomal subunit protein uS3
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
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Chain IDs:D (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Listeria innocua
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Gene (Uniprot):rpsE
Chain IDs:E (auth: e)
Chain Length:207
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 protein bS6
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 protein uS7
Gene (Uniprot):rpsG
Chain IDs:G (auth: g)
Chain Length:156
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 protein uS8
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 protein uS9
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 protein uS10
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 protein uS11
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 protein uS12
Gene (Uniprot):rpsL
Chain IDs:L (auth: l)
Chain Length:145
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 protein uS13
Gene (Uniprot):rpsM
Chain IDs:M (auth: m)
Chain Length:122
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 protein uS14
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 protein uS15
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 protein bS16
Gene (Uniprot):rpsP
Chain IDs:P (auth: p)
Chain Length:90
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 protein uS17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: q)
Chain Length:87
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 protein bS18
Gene (Uniprot):rpsR
Chain IDs:R (auth: r)
Chain Length:114
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 protein uS19
Gene (Uniprot):rpsS
Chain IDs:S (auth: s)
Chain Length:92
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 protein bS20
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:V (auth: v)
Chain Length:94
Number of Molecules:1
Biological Source:Listeria monocytogenes EGD-e
UniProt ID:Q8Y8Y0 Pfam ID:PF13167, PF16360, PF01926
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome hibernation promoting factor
Gene (Uniprot):raiA
Chain IDs:W (auth: w)
Chain Length:103
Number of Molecules:1
Biological Source:Listeria innocua
UniProt ID:A0A660JMK7 Pfam ID:PF02482, PF16321
Polymer Type:polyribonucleotide
Molecule: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
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
8UU7