6YPU

Acinetobacter baumannii ribosome-amikacin complex - 30S subunit body


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.

Nicholson, D.Edwards, T.A.O'Neill, A.J.Ranson, N.A.

(2020) Structure 28: 1087-1100.e3

  • DOI: https://doi.org/10.1016/j.str.2020.08.004
  • Primary Citation of Related Structures:  
    6YHS, 6YPU, 6YS5, 6YSI, 6YT9, 6YTF

  • PubMed Abstract: 

    Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2C [auth c]250Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CC74 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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UniProt GroupD0CC74
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth e]208Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD21 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth f]165Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD14 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth g]127Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C5Z0 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth i]131Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD11 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11H [auth l]128Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD20 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12I [auth m]124Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C9P6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15J [auth p]89Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CAU9 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16K [auth q]83Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CCR5 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17L [auth r]85Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD06 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18M [auth s]75Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C5Y9 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20N [auth u]88Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C7N1 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21O [auth v]71Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C5Q3 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0C5Q3 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth 2],
B [auth 4]
1,544Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKN (Subject of Investigation/LOI)
Query on AKN

Download Ideal Coordinates CCD File 
WB [auth 4](2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide
C22 H43 N5 O13
LKCWBDHBTVXHDL-RMDFUYIESA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 2]
AB [auth 2]
BA [auth 2]
BB [auth 2]
CA [auth 2]
AA [auth 2],
AB [auth 2],
BA [auth 2],
BB [auth 2],
CA [auth 2],
CB [auth 2],
DA [auth 2],
DB [auth 2],
EA [auth 2],
EB [auth 2],
FA [auth 2],
FB [auth 2],
GA [auth 2],
GB [auth 2],
HA [auth 2],
HB [auth 2],
IA [auth 2],
IB [auth 2],
JA [auth 2],
JB [auth 2],
KA [auth 2],
KB [auth 2],
LA [auth 2],
LB [auth 2],
MA [auth 2],
MB [auth 2],
NA [auth 2],
NB [auth 2],
OA [auth 2],
OB [auth 2],
P [auth 2],
PA [auth 2],
PB [auth 2],
Q [auth 2],
QA [auth 2],
QB [auth 4],
R [auth 2],
RA [auth 2],
RB [auth 4],
S [auth 2],
SA [auth 2],
SB [auth 4],
T [auth 2],
TA [auth 2],
TB [auth 4],
U [auth 2],
UA [auth 2],
UB [auth 4],
V [auth 2],
VA [auth 2],
VB [auth 4],
W [auth 2],
WA [auth 2],
X [auth 2],
XA [auth 2],
Y [auth 2],
YA [auth 2],
Z [auth 2],
ZA [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1-3660
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom203743/Z/16/Z
Wellcome TrustUnited Kingdom108466/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references