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:
Escherichia coli (Taxon ID: 562)
Vibrio alginolyticus (Taxon ID: 663)
Host Organism:
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
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:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6, fully modified isoform
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase HrpA
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL1
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS16
Gene (Uniprot):rpsP
Chain IDs:CA (auth: AO), VB (auth: I)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7T3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Gene (Uniprot):rpsT
Chain IDs:GA (auth: AS), HD (auth: u)
Chain Length:87
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7U7 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL31A
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:57
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2
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
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL9
Gene (Uniprot):rplI
Chain IDs:QA (auth: Ac), HC (auth: U)
Chain Length:149
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:RA (auth: Ad), IC (auth: V)
Chain Length:206
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15
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
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL17
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL19
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL20
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL21
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23
Gene (Uniprot):rplW
Chain IDs:CB (auth: Ao), TC (auth: g)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0ADZ0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL25
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL27
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL28
Gene (Uniprot):rpmB
Chain IDs:GB (auth: As), XC (auth: k)
Chain Length:87
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7M2 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL30
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL32
Gene (Uniprot):rpmF
Chain IDs:JB (auth: Av), AD (auth: n)
Chain Length:57
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7N4 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL33
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL34
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL35
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein bL36A
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:ATP-dependent RNA helicase HrpA
Gene (Uniprot):hrpA
Chain IDs:OB (auth: B)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
UniProt ID:P43329 Pfam ID:PF00270, PF00271, PF04408, PF21010, PF07717, PF11898
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
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
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL10
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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Chemical

Disease

Primary Citation of related structures
9GGR