6YHS

Acinetobacter baumannii ribosome-amikacin complex - 50S subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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. Electronic address: n.a.ranson@leeds.ac.uk.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2E [auth A]274Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplBHMPREF0010_02630
Find proteins for D0CD00 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3F [auth B]212Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplCHMPREF0010_02627
Find proteins for D0CCZ7 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4G [auth C]200Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplDHMPREF0010_02628
Find proteins for D0CCZ8 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5H [auth D]178Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplEHMPREF0010_02639
Find proteins for D0CD09 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6I [auth E]177Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplFHMPREF0010_02642
Find proteins for D0CD12 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth F]142Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplMHMPREF0010_03715
Find proteins for D0CG35 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth G]122Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplNHMPREF0010_02637
Find proteins for D0CD07 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth H]146Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplOHMPREF0010_02646
Find proteins for D0CD16 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth I]137Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplPHMPREF0010_02634
Find proteins for D0CD04 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth J]125Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplQHMPREF0010_02653
Find proteins for D0CD23 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth K]116Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplRHMPREF0010_02643
Find proteins for D0CD13 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth L]122Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplSHMPREF0010_02548
Find proteins for D0CCR8 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth M]119Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplTHMPREF0010_01656
Find proteins for D0CA76 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth N]103Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplUHMPREF0010_02886
Find proteins for D0CDQ6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth O]110Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplVHMPREF0010_02632
Find proteins for D0CD02 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth P]106Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplWHMPREF0010_02629
Find proteins for D0CCZ9 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth Q]105Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplXHMPREF0010_02638
Find proteins for D0CD08 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth R]98Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rplYHMPREF0010_01330
Find proteins for D0C9L7 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth S]85Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmAHMPREF0010_02887
Find proteins for D0CDQ7 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28X [auth T]78Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmBHMPREF0010_01790
Find proteins for D0CAL0 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth U]65Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmCHMPREF0010_02635
Find proteins for D0CD05 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth V]58Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmDHMPREF0010_02645
Find proteins for D0CD15 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth X]61Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmFHMPREF0010_01318
Find proteins for D0C9K5 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth Y]51Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmGHMPREF0010_01791
Find proteins for D0CAL1 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth Z]44Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmHHMPREF0010_03686
Find proteins for D0CG06 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth a]64Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmIHMPREF0010_01657
Find proteins for D0CA77 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth b]38Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
Gene Names: rpmJHMPREF0010_02648
Find proteins for D0CD18 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 1]2903Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth 5]117Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Entity ID: 3
MoleculeChainsLengthOrganismImage
E-site tRNAC [auth 6], D [auth 8]77Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
JG [auth b]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth 1] , AC [auth 1] , AD [auth 1] , AE [auth 1] , AF [auth 1] , AG [auth 1] , BB [auth 1] , BC [auth 1] , 
AB [auth 1],  AC [auth 1],  AD [auth 1],  AE [auth 1],  AF [auth 1],  AG [auth 1],  BB [auth 1],  BC [auth 1],  BD [auth 1],  BE [auth 1],  BF [auth 1],  BG [auth 1],  CB [auth 1],  CC [auth 1],  CD [auth 1],  CE [auth 1],  CF [auth 1],  CG [auth 1],  DB [auth 1],  DC [auth 1],  DD [auth 1],  DE [auth 1],  DF [auth 1],  DG [auth 1],  EB [auth 1],  EC [auth 1],  ED [auth 1],  EE [auth 1],  EF [auth 1],  EG [auth 1],  FA [auth 1],  FB [auth 1],  FC [auth 1],  FD [auth 1],  FE [auth 1],  FF [auth 1],  FG [auth 1],  GA [auth 1],  GB [auth 1],  GC [auth 1],  GD [auth 1],  GE [auth 1],  GF [auth 1],  GG [auth 5],  HA [auth 1],  HB [auth 1],  HC [auth 1],  HD [auth 1],  HE [auth 1],  HF [auth 1],  HG [auth 5],  IA [auth 1],  IB [auth 1],  IC [auth 1],  ID [auth 1],  IE [auth 1],  IF [auth 1],  IG [auth 5],  JA [auth 1],  JB [auth 1],  JC [auth 1],  JD [auth 1],  JE [auth 1],  JF [auth 1],  KA [auth 1],  KB [auth 1],  KC [auth 1],  KD [auth 1],  KE [auth 1],  KF [auth 1],  LA [auth 1],  LB [auth 1],  LC [auth 1],  LD [auth 1],  LE [auth 1],  LF [auth 1],  MA [auth 1],  MB [auth 1],  MC [auth 1],  MD [auth 1],  ME [auth 1],  MF [auth 1],  NA [auth 1],  NB [auth 1],  NC [auth 1],  ND [auth 1],  NE [auth 1],  NF [auth 1],  OA [auth 1],  OB [auth 1],  OC [auth 1],  OD [auth 1],  OE [auth 1],  OF [auth 1],  PA [auth 1],  PB [auth 1],  PC [auth 1],  PD [auth 1],  PE [auth 1],  PF [auth 1],  QA [auth 1],  QB [auth 1],  QC [auth 1],  QD [auth 1],  QE [auth 1],  QF [auth 1],  RA [auth 1],  RB [auth 1],  RC [auth 1],  RD [auth 1],  RE [auth 1],  RF [auth 1],  SA [auth 1],  SB [auth 1],  SC [auth 1],  SD [auth 1],  SE [auth 1],  SF [auth 1],  TA [auth 1],  TB [auth 1],  TC [auth 1],  TD [auth 1],  TE [auth 1],  TF [auth 1],  UA [auth 1],  UB [auth 1],  UC [auth 1],  UD [auth 1],  UE [auth 1],  UF [auth 1],  VA [auth 1],  VB [auth 1],  VC [auth 1],  VD [auth 1],  VE [auth 1],  VF [auth 1],  WA [auth 1],  WB [auth 1],  WC [auth 1],  WD [auth 1],  WE [auth 1],  WF [auth 1],  XA [auth 1],  XB [auth 1],  XC [auth 1],  XD [auth 1],  XE [auth 1],  XF [auth 1],  YA [auth 1],  YB [auth 1],  YC [auth 1],  YD [auth 1],  YE [auth 1],  YF [auth 1],  ZA [auth 1],  ZB [auth 1],  ZC [auth 1],  ZD [auth 1],  ZE [auth 1],  ZF [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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