6YSI

Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 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: 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: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2274Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD00 (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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3212Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CCZ7 (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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4200Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CCZ8 (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
50S ribosomal protein L5178Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD09 (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
50S ribosomal protein L6177Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD12 (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
50S ribosomal protein L13142Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CG35 (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
50S ribosomal protein L14122Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD07 (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
50S ribosomal protein L15146Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD16 (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
50S ribosomal protein L16137Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD04 (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
50S ribosomal protein L17125Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD23 (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
50S ribosomal protein L18116Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD13 (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
50S ribosomal protein L19122Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CCR8 (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
50S ribosomal protein L20119Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CA76 (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
50S ribosomal protein L21103Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CDQ6 (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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22110Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD02 (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: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23106Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CCZ9 (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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24105Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD08 (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: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2598Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C9L7 (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: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2785Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CDQ7 (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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2878Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CAL0 (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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2965Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD05 (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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3058Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD15 (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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3174Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CBZ8 (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: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3261Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0C9K5 (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: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3351Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CAL1 (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: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3444Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CG06 (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: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth a]64Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CA77 (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: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth b]38Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841Mutation(s): 0 
UniProt
Find proteins for D0CD18 (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: 27
MoleculeChains LengthOrganismImage
23S ribosomal RNAAA [auth 1]2,903Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Entity ID: 28
MoleculeChains LengthOrganismImage
5S ribosomal RNABA [auth 5]117Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Entity ID: 29
MoleculeChains LengthOrganismImage
E-site tRNACA [auth 6],
DA [auth 8]
77Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T1C (Subject of Investigation/LOI)
Query on T1C

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JG [auth 1],
KG [auth 5],
OG [auth 5]
TIGECYCLINE
C29 H41 N5 O8
FPZLLRFZJZRHSY-HJYUBDRYSA-P
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
AB [auth 1]
AC [auth 1]
AD [auth 1]
AE [auth 1]
AF [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],
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 1],
HA [auth 1],
HB [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
IA [auth 1],
IB [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
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],
LG [auth 5],
MA [auth 1],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 5],
NA [auth 1],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 5],
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1-3660
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



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