8CGJ

Streptomycin bound to the 30S body


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural conservation of antibiotic interaction with ribosomes.

Paternoga, H.Crowe-McAuliffe, C.Bock, L.V.Koller, T.O.Morici, M.Beckert, B.Myasnikov, A.G.Grubmuller, H.Novacek, J.Wilson, D.N.

(2023) Nat Struct Mol Biol 30: 1380-1392

  • DOI: https://doi.org/10.1038/s41594-023-01047-y
  • Primary Citation of Related Structures:  
    8CA7, 8CAI, 8CAM, 8CAZ, 8CEP, 8CEU, 8CF1, 8CF8, 8CGD, 8CGI, 8CGJ, 8CGK, 8CGR, 8CGU, 8CGV

  • PubMed Abstract: 

    The ribosome is a major target for clinically used antibiotics, but multidrug resistant pathogenic bacteria are making our current arsenal of antimicrobials obsolete. Here we present cryo-electron-microscopy structures of 17 distinct compounds from six different antibiotic classes bound to the bacterial ribosome at resolutions ranging from 1.6 to 2.2 Å. The improved resolution enables a precise description of antibiotic-ribosome interactions, encompassing solvent networks that mediate multiple additional interactions between the drugs and their target. Our results reveal a high structural conservation in the binding mode between antibiotics with the same scaffold, including ordered water molecules. Water molecules are visualized within the antibiotic binding sites that are preordered, become ordered in the presence of the drug and that are physically displaced on drug binding. Insight into RNA-ligand interactions will facilitate development of new antimicrobial agents, as well as other RNA-targeting therapies.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2241Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3233Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4206Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5167Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS6, non-modified isoform131Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8G [auth H]130Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11H [auth K]129Escherichia coli BW25113Mutation(s): 1 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12I [auth L]124Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15J [auth O]89Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16K [auth P]82Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17L [auth Q]84Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS18M [auth R]75Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21N [auth U]71Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20O [auth T]87Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,540Escherichia coli BW25113
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Entity ID: 16
MoleculeChains LengthOrganismImage
23S rRNAP [auth a]2,904Escherichia coli BW25113
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5I0 (Subject of Investigation/LOI)
Query on 5I0

Download Ideal Coordinates CCD File 
S [auth A][(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium
C21 H44 N7 O13
ATLHDHNZEMANQF-UQHZJGBMSA-Q
TAC (Subject of Investigation/LOI)
Query on TAC

Download Ideal Coordinates CCD File 
T [auth A]TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BD [auth F]
CC [auth A]
DC [auth A]
EC [auth A]
FC [auth A]
BD [auth F],
CC [auth A],
DC [auth A],
EC [auth A],
FC [auth A],
GC [auth A],
HC [auth A],
IC [auth A],
JC [auth A],
KC [auth A],
LC [auth A],
MC [auth A],
NC [auth A],
OC [auth A],
PC [auth A],
Q [auth A],
QC [auth A],
R [auth A],
RC [auth A],
SC [auth A],
TC [auth A],
UC [auth A],
VC [auth A],
WC [auth A],
XC [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
BA [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
CA [auth A],
CB [auth A],
DA [auth A],
DB [auth A],
EA [auth A],
EB [auth A],
FA [auth A],
FB [auth A],
GA [auth A],
GB [auth A],
HA [auth A],
HB [auth A],
IA [auth A],
IB [auth A],
JA [auth A],
JB [auth A],
KA [auth A],
KB [auth A],
LA [auth A],
LB [auth A],
MA [auth A],
MB [auth A],
NA [auth A],
NB [auth A],
OA [auth A],
OB [auth A],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
U [auth A],
UA [auth A],
UB [auth A],
V [auth A],
VA [auth A],
VB [auth A],
W [auth A],
WA [auth A],
WB [auth A],
X [auth A],
XA [auth A],
XB [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
I [auth L]L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0415

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentDLR01Kl1820
iNEXT-DiscoveryEuropean Union871037
Other governmentLM2018127

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-09
    Changes: Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-20
    Changes: Database references
  • Version 1.4: 2023-11-15
    Changes: Data collection, Derived calculations
  • Version 1.5: 2024-04-24
    Changes: Data collection