4WOI image
Deposition Date 2014-10-15
Release Date 2015-08-05
Last Version Date 2024-11-13
Entry Detail
PDB ID:
4WOI
Keywords:
Title:
4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.25
R-Value Work:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA), JC (auth: DA)
Chain Length:1542
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), KC (auth: DB)
Chain Length:241
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), LC (auth: DC)
Chain Length:233
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), MC (auth: DD)
Chain Length:206
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), NC (auth: DE)
Chain Length:167
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), OC (auth: DF)
Chain Length:135
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), PC (auth: DG)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: AH), QC (auth: DH)
Chain Length:130
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), RC (auth: DI)
Chain Length:130
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), SC (auth: DJ)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), TC (auth: DK)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), UC (auth: DL)
Chain Length:124
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), VC (auth: DM)
Chain Length:118
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N (auth: AN), WC (auth: DN)
Chain Length:101
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:O (auth: AO), XC (auth: DO)
Chain Length:89
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), YC (auth: DP)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: AQ), ZC (auth: DQ)
Chain Length:84
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), AD (auth: DR)
Chain Length:75
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), BD (auth: DS)
Chain Length:92
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), CD (auth: DT)
Chain Length:87
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), DD (auth: DU)
Chain Length:71
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:Ribosome-recycling factor
Gene (Uniprot):frr
Chain IDs:V (auth: AV)
Chain Length:185
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:Messenger RNA
Chain IDs:W (auth: AW), ED (auth: DV)
Chain Length:16
Number of Molecules:2
Biological Source:Enterobacteria phage L1
Polymer Type:polyribonucleotide
Molecule:Phenylalanine specific transfer RNA, tRNA-Phe
Chain IDs:X (auth: AX), FD (auth: DW)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:YA (auth: B0), EC (auth: C0)
Chain Length:57
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:ZA (auth: B1), FC (auth: C1)
Chain Length:55
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:AB (auth: B2), GC (auth: C2)
Chain Length:46
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:BB (auth: B3), HC (auth: C3)
Chain Length:65
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:CB (auth: B4), IC (auth: C4)
Chain Length:38
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:DB (auth: B5)
Chain Length:228
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Y (auth: BA), EB (auth: CA)
Chain Length:2904
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Z (auth: BB), FB (auth: CB)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli str. K-12 substr. MDS42
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: BC), GB (auth: CC)
Chain Length:273
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:BA (auth: BD), HB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: BE), IB (auth: CE)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: BF), JB (auth: CF)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:EA (auth: BG), KB (auth: CG)
Chain Length:177
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: BH), LB (auth: CH)
Chain Length:149
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:GA (auth: BI), MB (auth: CI)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:HA (auth: BJ), NB (auth: CJ)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:IA (auth: BK), OB (auth: CK)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:JA (auth: BL), PB (auth: CL)
Chain Length:144
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:KA (auth: BM), QB (auth: CM)
Chain Length:136
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: BN), RB (auth: CN)
Chain Length:127
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:MA (auth: BO), SB (auth: CO)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:NA (auth: BP), TB (auth: CP)
Chain Length:115
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:OA (auth: BQ), UB (auth: CQ)
Chain Length:118
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:PA (auth: BR), VB (auth: CR)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:QA (auth: BS), WB (auth: CS)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:RA (auth: BT), XB (auth: CT)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:SA (auth: BU), YB (auth: CU)
Chain Length:104
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:TA (auth: BV), ZB (auth: CV)
Chain Length:94
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: BW), AC (auth: CW)
Chain Length:85
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: BX), BC (auth: CX)
Chain Length:78
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: BY), CC (auth: CY)
Chain Length:63
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: BZ), DC (auth: CZ)
Chain Length:59
Number of Molecules:2
Biological Source:Escherichia coli
Primary Citation
Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.
Nat Commun 6 7896 7896 (2015)
PMID: 26224058 DOI: 10.1038/ncomms8896

Abstact

Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures