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- PDB-6ys5: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head -

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Basic information

Entry
Database: PDB / ID: 6ys5
TitleAcinetobacter baumannii ribosome-amikacin complex - 30S subunit head
Components
  • (30S ribosomal protein ...) x 7
  • 16S ribosomal RNA
  • E-site tRNA
  • mRNAMessenger RNA
KeywordsRIBOSOME / antibiotic / amikacin / translation
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein S14, bacterial/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S9, bacterial/plastid / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13-like, H2TH / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ribosomal protein S9 signature. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 30S ribosomal protein S7 / 30S ribosomal protein S10 / 30S ribosomal protein S19 / 30S ribosomal protein S3 / 30S ribosomal protein S14 / 30S ribosomal protein S13 / 30S ribosomal protein S9
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsNicholson, D. / Edwards, T.A. / O'Neill, A.J. / Ranson, N.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust203743/Z/16/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Structure / Year: 2020
Title: Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Authors: David Nicholson / Thomas A Edwards / Alex J O'Neill / Neil A Ranson /
Abstract: Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and ...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.
History
DepositionApr 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
3: 16S ribosomal RNA
7: E-site tRNA
9: mRNA
d: 30S ribosomal protein S3
h: 30S ribosomal protein S7
j: 30S ribosomal protein S9
k: 30S ribosomal protein S10
n: 30S ribosomal protein S13
o: 30S ribosomal protein S14
t: 30S ribosomal protein S19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)632,88934
Polymers632,30610
Non-polymers58324
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35750 Å2
ΔGint-479 kcal/mol
Surface area97490 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules 379

#1: RNA chain 16S ribosomal RNA /


Mass: 500126.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
#2: RNA chain E-site tRNA


Mass: 24346.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
#3: RNA chain mRNA / Messenger RNA


Mass: 1179.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Mixture of mRNAs at the E-site, modelled as polyuridine
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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30S ribosomal protein ... , 7 types, 7 molecules dhjknot

#4: Protein 30S ribosomal protein S3 /


Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CD03
#5: Protein 30S ribosomal protein S7 /


Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 126-145 modelled without side chains
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0C9P7
#6: Protein 30S ribosomal protein S9 /


Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CG36
#7: Protein 30S ribosomal protein S10 /


Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CCZ6
#8: Protein 30S ribosomal protein S13 /


Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CD19
#9: Protein 30S ribosomal protein S14 /


Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CD10
#10: Protein 30S ribosomal protein S19 /


Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CD01

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Non-polymers , 1 types, 24 molecules

#11: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Acinetobacter baumannii ribosome-amikacin complex - 30S subunit head
Type: RIBOSOME / Entity ID: #1-#10 / Source: NATURAL
Source (natural)Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 10 sec. / Electron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 50

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategory
4Gctf1.18CTF correction
7UCSF ChimeraX-0.9model fitting
9PHENIX1.17.1-3660model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51958
Details: Multi-body refinement was carried out in RELION 3.0 to obtain the final '30S subunit head' reconstruction. The mask used for this procedure is deposited with this entry.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
15MDZ

5mdz

1
25AFI

5afi

w1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007318137
ELECTRON MICROSCOPYf_angle_d0.702326812
ELECTRON MICROSCOPYf_chiral_restr0.04583413
ELECTRON MICROSCOPYf_plane_restr0.0051645
ELECTRON MICROSCOPYf_dihedral_angle_d15.80276665

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