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- PDB-6yt9: Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni... -

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Basic information

Entry
Database: PDB / ID: 6yt9
TitleAcinetobacter baumannii ribosome-tigecycline complex - 30S subunit body
Components
  • (30S ribosomal protein ...) x 13
  • 16S ribosomal RNA
KeywordsRIBOSOME / antibiotic / tigecycline / translation
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S11 / S4 RNA-binding domain / S4 domain / Ribosomal protein S11 / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Ribosomal protein S12 signature. / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / Ribosomal protein S11 superfamily / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS21 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS4
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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 24, 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
Revision 1.2May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-10914
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
2: 16S ribosomal RNA
4: 16S ribosomal RNA
c: 30S ribosomal protein S2
e: 30S ribosomal protein S4
f: 30S ribosomal protein S5
g: 30S ribosomal protein S6
i: 30S ribosomal protein S8
l: 30S ribosomal protein S11
m: 30S ribosomal protein S12
p: 30S ribosomal protein S15
q: 30S ribosomal protein S16
r: 30S ribosomal protein S17
s: 30S ribosomal protein S18
u: 30S ribosomal protein S20
v: 30S ribosomal protein S21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,182,49271
Polymers1,181,13115
Non-polymers1,36156
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 13 types, 13 molecules cefgilmpqrsuv

#2: Protein 30S ribosomal protein S2


Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modelled without side chains / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CC74
#3: Protein 30S ribosomal protein S4


Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: residues 23-30 and 43-51 modelled without side chains
Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CD21
#4: Protein 30S ribosomal protein S5


Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CD14
#5: Protein 30S ribosomal protein S6


Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0C5Z0
#6: Protein 30S ribosomal protein S8


Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CD11
#7: Protein 30S ribosomal protein S11


Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CD20
#8: Protein 30S ribosomal protein S12


Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0C9P6
#9: Protein 30S ribosomal protein S15


Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CAU9
#10: Protein 30S ribosomal protein S16


Mass: 9215.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CCR5
#11: Protein 30S ribosomal protein S17


Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0CD06
#12: Protein 30S ribosomal protein S18


Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0C5Y9
#13: Protein 30S ribosomal protein S20


Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0C7N1
#14: Protein 30S ribosomal protein S21


Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 2-36 modelled without side chains / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: D0C5Q3

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RNA chain / Non-polymers , 2 types, 58 molecules 24

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


Mass: 24.305 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: Mg
#1: RNA chain 16S ribosomal RNA


Mass: 500126.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: GenBank: 692328596

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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-tigecycline complex - 30S subunit body
Type: RIBOSOME / Entity ID: #1-#14 / Source: NATURAL
Source (natural)Organism: Acinetobacter baumannii (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 FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 1.1 sec. / Electron dose: 62 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231159
Details: Multi-body refinement was carried out in RELION 3.0 to obtain the final '30S subunit body' 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

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
15MDZ

5mdz

5MDZ1
25AFI

5afi

w5AFI2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 11.33 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009736036
ELECTRON MICROSCOPYf_angle_d0.793853896
ELECTRON MICROSCOPYf_chiral_restr0.04856919
ELECTRON MICROSCOPYf_plane_restr0.00552986
ELECTRON MICROSCOPYf_dihedral_angle_d15.937714100

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