ISDA

Deposition Date 2023-10-31

Release Date 2024-02-28

Last Version Date 2024-05-08

Entry Detail

PDB ID:

8UU8

Keywords:

RIBOSOME

Title:

Cryo-EM structure of the Listeria innocua 70S ribosome (head-swiveled) in complex with HflXr and pe/E-tRNA (structure II-C)

Biological Source:

Source Organism:

Escherichia phage T4 (Taxon ID: 2681598)
Listeria innocua (Taxon ID: 1642)
Escherichia coli (Taxon ID: 562)
Listeria monocytogenes EGD-e (Taxon ID: 169963)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.10 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
Gene (Uniprot):rpmC
Chain IDs:UA (auth: 1)
Chain Length:63
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5AGL9 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
Gene (Uniprot):rpmD
Chain IDs:VA (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U4VSJ1 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31B
Gene (Uniprot):rpsU
Chain IDs:WA (auth: 3)
Chain Length:81
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U4MT39 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:XA (auth: 4)
Chain Length:57
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JNN0 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
Gene (Uniprot):rpmG
Chain IDs:YA (auth: 5)
Chain Length:49
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JRA4 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
Gene (Uniprot):rpmH
Chain IDs:ZA (auth: 6)
Chain Length:44
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JKZ6 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
Gene (Uniprot):rpmI
Chain IDs:AB (auth: 7)
Chain Length:66
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JIB9 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36
Gene (Uniprot):rpmJ
Chain IDs:BB (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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
Gene (Uniprot):rplB
Chain IDs:Z (auth: C)
Chain Length:218
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5A742 Pfam ID:PF00181, PF03947

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

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

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL11
Gene (Uniprot):rplK
Chain IDs:FA (auth: H)
Chain Length:141
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JML6 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10
Gene (Uniprot):rplJ
Chain IDs:EA (auth: I)
Chain Length:130
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5A6T9 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
Gene (Uniprot):rplM
Chain IDs:GA (auth: L)
Chain Length:145
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5AGN0 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
Gene (Uniprot):rplN
Chain IDs:HA (auth: M)
Chain Length:121
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5AP82 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
Gene (Uniprot):rplO
Chain IDs:IA (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5A6S7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16
Gene (Uniprot):rplP
Chain IDs:JA (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U4VSU8 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
Gene (Uniprot):rplQ
Chain IDs:KA (auth: P)
Chain Length:90
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U4VSW3 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
Gene (Uniprot):rplR
Chain IDs:LA (auth: Q)
Chain Length:87
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5AR65 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
Gene (Uniprot):rplS
Chain IDs:MA (auth: R)
Chain Length:79
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A6B0JQF2 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
Gene (Uniprot):rplT
Chain IDs:NA (auth: S)
Chain Length:119
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JH71 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
Gene (Uniprot):rplU
Chain IDs:OA (auth: T)
Chain Length:102
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5AD18 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
Gene (Uniprot):rplV
Chain IDs:PA (auth: U)
Chain Length:118
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5ANW2 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:QA (auth: V)
Chain Length:94
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U4MTC5 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
Gene (Uniprot):rplX
Chain IDs:RA (auth: W)
Chain Length:103
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5AD05 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
Gene (Uniprot):rpmA
Chain IDs:SA (auth: Y)
Chain Length:96
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JMC7 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:TA (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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Gene (Uniprot):rpsC
Chain IDs:C (auth: c)
Chain Length:218
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

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

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Gene (Uniprot):rpsH
Chain IDs:H (auth: h)
Chain Length:141
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A0U5A6U3 Pfam ID:PF00410

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

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

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
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

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

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

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:T (auth: t)
Chain Length:102
Number of Molecules:1
Biological Source:Listeria innocua

UniProt ID:A0A660JML5 Pfam ID:PF01649

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 Phenylalanine tRNA
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
4SU	U	U	modified residue
5MU	U	U	modified residue
G7M	U	G	modified residue
MIA	U	A	modified residue
PSU	U	U	modified residue

Ligand Molecules

GCP

Primary Citation

Mechanistic insights into the alternative ribosome recycling by HflXr.

Seely, S.M, Basu, R.S, Gagnon, M.G.Show

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures