6YSI image
Entry Detail
PDB ID:
6YSI
EMDB ID:
Keywords:
Title:
Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit
Biological Source:
PDB Version:
Deposition Date:
2020-04-22
Release Date:
2020-09-16
Method Details:
Experimental Method:
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:AA (auth: 1)
Chain Length:2903
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:BA (auth: 5)
Chain Length:117
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polyribonucleotide
Description:E-site tRNA
Chain IDs:CA (auth: 6), DA (auth: 8)
Chain Length:77
Number of Molecules:2
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:A
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:B
Chain Length:212
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:C
Chain Length:200
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:D
Chain Length:178
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:E
Chain Length:177
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:F
Chain Length:142
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:G
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:I
Chain Length:137
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:J
Chain Length:125
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:K
Chain Length:116
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:L
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:M
Chain Length:119
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:N
Chain Length:103
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:O
Chain Length:110
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:P
Chain Length:106
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:Q
Chain Length:105
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:R
Chain Length:98
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:S
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:T
Chain Length:78
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:U
Chain Length:65
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:V
Chain Length:58
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:W
Chain Length:74
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:X
Chain Length:61
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:Y
Chain Length:51
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:Z
Chain Length:44
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:EA (auth: a)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:FA (auth: b)
Chain Length:212
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Primary Citation
Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Structure 28 1087 1100.e3 (2020)
PMID: 32857965 DOI: 10.1016/j.str.2020.08.004

Abstact

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.

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Primary Citation of related structures