6YHS image
Deposition Date 2020-03-30
Release Date 2020-09-16
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6YHS
Keywords:
Title:
Acinetobacter baumannii ribosome-amikacin complex - 50S subunit
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: 1)
Chain Length:2903
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: 5)
Chain Length:117
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:C (auth: 6), D (auth: 8)
Chain Length:77
Number of Molecules:2
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:E (auth: A)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:F (auth: B)
Chain Length:38
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:G (auth: C)
Chain Length:200
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:H (auth: D)
Chain Length:178
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:I (auth: E)
Chain Length:177
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:J (auth: F)
Chain Length:142
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:K (auth: G)
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:L (auth: H)
Chain Length:146
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:M (auth: I)
Chain Length:137
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:N (auth: J)
Chain Length:125
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:O (auth: K)
Chain Length:116
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:P (auth: L)
Chain Length:122
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:Q (auth: M)
Chain Length:119
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:R (auth: N)
Chain Length:103
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:S (auth: O)
Chain Length:110
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:T (auth: P)
Chain Length:106
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:U (auth: Q)
Chain Length:105
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:V (auth: R)
Chain Length:98
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:W (auth: S)
Chain Length:85
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:X (auth: T)
Chain Length:78
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:Y (auth: U)
Chain Length:65
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Z (auth: V)
Chain Length:58
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: X)
Chain Length:61
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: Y)
Chain Length:51
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: Z)
Chain Length:44
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: a)
Chain Length:274
Number of Molecules:1
Biological Source:Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: b)
Chain Length:38
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