9GGR image
Deposition Date 2024-08-14
Release Date 2025-02-12
Last Version Date 2025-03-19
Entry Detail
PDB ID:
9GGR
Keywords:
RIBOSOME
Title:
Structure of the HrpA-bound E. coli disome, Class II
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Vibrio alginolyticus (Taxon ID: 663)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9GGR validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: 0), O (auth: AA)
Chain Length:1542
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsB
Chain IDs:B (auth: 1), P (auth: AB)
Chain Length:241
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7V0 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: 2), Q (auth: AC)
Chain Length:233
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7V3 Pfam ID:PF00189, PF07650
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsD
Chain IDs:D (auth: 3), R (auth: AD)
Chain Length:206
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7V8 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: 4), S (auth: AE)
Chain Length:167
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7W1 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: 5), T (auth: AF)
Chain Length:135
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P02358 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: 6), U (auth: AG)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P02359 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: 7), V (auth: AH)
Chain Length:130
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7W7 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: 8), W (auth: AI)
Chain Length:130
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7X3 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: 9), X (auth: AJ)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7R5 Pfam ID:PF00338
Polymer Type:polyribonucleotide
Molecule:A-site tRNA
Chain IDs:K (auth: A)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsU
Chain IDs:L (auth: A1), ID (auth: v)
Chain Length:71
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P68679 Pfam ID:PF01165
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase Hr
Gene (Uniprot):hrpA
Chain IDs:M (auth: A2)
Chain Length:1300
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P43329 Pfam ID:PF00270, PF00271, PF04408, PF21010, PF07717, PF11898
Polymer Type:polyribonucleotide
Molecule:A-site tRNA
Chain IDs:N (auth: A3)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplA
Chain IDs:Y (auth: AK), PB (auth: C)
Chain Length:115
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7L0 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsM
Chain IDs:Z (auth: AL), SB (auth: F)
Chain Length:118
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7S9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsN
Chain IDs:AA (auth: AM), TB (auth: G)
Chain Length:101
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AG59 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsO
Chain IDs:BA (auth: AN), UB (auth: H)
Chain Length:89
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0ADZ4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsP
Chain IDs:CA (auth: AO), VB (auth: I)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7T3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:DA (auth: AP), WB (auth: J)
Chain Length:84
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AG63 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsR
Chain IDs:EA (auth: AQ), XB (auth: K)
Chain Length:75
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7T7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsS
Chain IDs:FA (auth: AR), GD (auth: t)
Chain Length:92
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7U3 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsT
Chain IDs:GA (auth: AS), HD (auth: u)
Chain Length:78
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7U7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmE
Chain IDs:HA (auth: AT), YB (auth: L)
Chain Length:70
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7M9 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:IA (auth: AU)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:JA (auth: AV), AC (auth: N)
Chain Length:2903
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:KA (auth: AW), BC (auth: O)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:LA (auth: AX), CC (auth: P)
Chain Length:273
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:MA (auth: AY), DC (auth: Q)
Chain Length:65
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:NA (auth: AZ), EC (auth: R)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplE
Chain IDs:OA (auth: Aa), FC (auth: S)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P62399 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:PA (auth: Ab), GC (auth: T)
Chain Length:177
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplI
Chain IDs:QA (auth: Ac), HC (auth: U)
Chain Length:233
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:RA (auth: Ad), IC (auth: V)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:SA (auth: Ae), JC (auth: W)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplN
Chain IDs:TA (auth: Af), KC (auth: X)
Chain Length:135
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplO
Chain IDs:UA (auth: Ag), LC (auth: Y)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:VA (auth: Ah), MC (auth: Z)
Chain Length:136
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:WA (auth: Ai), NC (auth: a)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplR
Chain IDs:XA (auth: Aj), OC (auth: b)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplS
Chain IDs:YA (auth: Ak), PC (auth: c)
Chain Length:115
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7K6 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplT
Chain IDs:ZA (auth: Al), QC (auth: d)
Chain Length:118
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:AB (auth: Am), RC (auth: e)
Chain Length:101
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:BB (auth: An), SC (auth: f)
Chain Length:89
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplW
Chain IDs:CB (auth: Ao), TC (auth: g)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplX
Chain IDs:DB (auth: Ap), UC (auth: h)
Chain Length:84
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplY
Chain IDs:EB (auth: Aq), VC (auth: i)
Chain Length:75
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:FB (auth: Ar), WC (auth: j)
Chain Length:92
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmB
Chain IDs:GB (auth: As), XC (auth: k)
Chain Length:78
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmC
Chain IDs:HB (auth: At), YC (auth: l)
Chain Length:70
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7M6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmD
Chain IDs:IB (auth: Au), ZC (auth: m)
Chain Length:59
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0AG51 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:JB (auth: Av), AD (auth: n)
Chain Length:2903
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7N4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG
Chain IDs:KB (auth: Aw), BD (auth: o)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmH
Chain IDs:LB (auth: Ax), CD (auth: p)
Chain Length:273
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmI
Chain IDs:MB (auth: Ay), DD (auth: q)
Chain Length:65
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmJ
Chain IDs:NB (auth: Az), ED (auth: r)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7Q6 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase Hr
Gene (Uniprot):hrpA
Chain IDs:OB (auth: B)
Chain Length:1326
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P43329 Pfam ID:PF00270, PF00271, PF04408, PF21010, PF07717, PF11898
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsK
Chain IDs:QB (auth: D), LD (auth: y)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7R9 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsL
Chain IDs:RB (auth: E), MD (auth: z)
Chain Length:124
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7S3 Pfam ID:PF00164
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:ZB (auth: M)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:VemP nascent chain
Chain IDs:FD (auth: s)
Chain Length:179
Number of Molecules:1
Biological Source:Vibrio alginolyticus
UniProt ID:A0A2I3CPK5
Polymer Type:polyribonucleotide
Molecule:messenger RNA
Chain IDs:JD (auth: w)
Chain Length:57
Number of Molecules:1
Biological Source:Vibrio alginolyticus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplJ
Chain IDs:KD (auth: x)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P0A7J3 Pfam ID:PF00466
Ligand Molecules
NA
Primary Citation
The RNA helicase HrpA rescues collided ribosomes in E. coli.
Mol.Cell 85 999 1007.e7 (2025)
PMID: 39922193 DOI: 10.1016/j.molcel.2025.01.018

Abstact

Although many antibiotics inhibit bacterial ribosomes, the loss of known factors that rescue stalled ribosomes does not lead to robust antibiotic sensitivity in E. coli, suggesting the existence of additional mechanisms. Here, we show that the RNA helicase HrpA rescues stalled ribosomes in E. coli. Acting selectively on ribosomes that have collided, HrpA uses ATP hydrolysis to split stalled ribosomes into subunits. Cryoelectron microscopy (cryo-EM) structures reveal how HrpA simultaneously binds to two collided ribosomes, explaining its selectivity, and how its helicase module engages downstream mRNA such that, by exerting a pulling force on the mRNA, it would destabilize the stalled ribosome. These studies show that ribosome splitting is a conserved mechanism that allows proteobacteria to tolerate ribosome-targeting antibiotics.

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Primary Citation of related structures
9GGR
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