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- PDB-6yhs: Acinetobacter baumannii ribosome-amikacin complex - 50S subunit -

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Basic information

Entry
Database: PDB / ID: 6yhs
TitleAcinetobacter baumannii ribosome-amikacin complex - 50S subunit
Components
  • (50S ribosomal protein ...) x 27
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-site tRNA
KeywordsRIBOSOME / antibiotic / amikacin / translation
Function / homology
Function and homology information


ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...ribosomal large subunit assembly / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 ...Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L5 / Ribosomal protein L6, alpha-beta domain / ribosomal L5P family C-terminus / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L6 / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif.
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L20 / 50S ribosomal protein L35 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 50S ribosomal protein L32 / 50S ribosomal protein L25 / 50S ribosomal protein L20 / 50S ribosomal protein L35 / 50S ribosomal protein L28 / 50S ribosomal protein L33 / 50S ribosomal protein L19 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 50S ribosomal protein L22 / 50S ribosomal protein L16 / 50S ribosomal protein L29 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L30 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 50S ribosomal protein L34 / 50S ribosomal protein L13
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (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
DepositionMar 30, 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
1: 23S ribosomal RNA
5: 5S ribosomal RNA
6: E-site tRNA
8: E-site tRNA
A: 50S ribosomal protein L2
B: 50S ribosomal protein L3
C: 50S ribosomal protein L4
D: 50S ribosomal protein L5
E: 50S ribosomal protein L6
F: 50S ribosomal protein L13
G: 50S ribosomal protein L14
H: 50S ribosomal protein L15
I: 50S ribosomal protein L16
J: 50S ribosomal protein L17
K: 50S ribosomal protein L18
L: 50S ribosomal protein L19
M: 50S ribosomal protein L20
N: 50S ribosomal protein L21
O: 50S ribosomal protein L22
P: 50S ribosomal protein L23
Q: 50S ribosomal protein L24
R: 50S ribosomal protein L25
S: 50S ribosomal protein L27
T: 50S ribosomal protein L28
U: 50S ribosomal protein L29
V: 50S ribosomal protein L30
X: 50S ribosomal protein L32
Y: 50S ribosomal protein L33
Z: 50S ribosomal protein L34
a: 50S ribosomal protein L35
b: 50S ribosomal protein L36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,377,779192
Polymers1,373,82531
Non-polymers3,954161
Water0
1


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

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Components

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RNA chain , 3 types, 4 molecules 1568

#1: RNA chain 23S ribosomal RNA /


Mass: 940330.125 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: GenBank: 1188467441
#2: RNA chain 5S ribosomal RNA /


Mass: 37608.344 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: GenBank: 1560725104
#3: RNA chain E-site tRNA


Mass: 24346.498 Da / Num. of mol.: 2 / 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)

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50S ribosomal protein ... , 27 types, 27 molecules ABCDEFGHIJKLMNOPQRSTUVXYZab

#4: Protein 50S ribosomal protein L2 /


Mass: 30319.092 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: D0CD00
#5: Protein 50S ribosomal protein L3 /


Mass: 22512.639 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: D0CCZ7
#6: Protein 50S ribosomal protein L4 /


Mass: 21583.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 2-12 modelled without side chains
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CCZ8
#7: Protein 50S ribosomal protein L5 /


Mass: 20051.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: modelled without side chains
Source: (natural) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
References: UniProt: D0CD09
#8: Protein 50S ribosomal protein L6 /


Mass: 19126.047 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: D0CD12
#9: Protein 50S ribosomal protein L13 /


Mass: 15951.440 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: D0CG35
#10: Protein 50S ribosomal protein L14 /


Mass: 13523.863 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: D0CD07
#11: Protein 50S ribosomal protein L15 /


Mass: 15509.915 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: D0CD16
#12: Protein 50S ribosomal protein L16 /


Mass: 15498.312 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: D0CD04
#13: Protein 50S ribosomal protein L17 /


Mass: 14021.230 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: D0CD23
#14: Protein 50S ribosomal protein L18 /


Mass: 12443.341 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: D0CD13
#15: Protein 50S ribosomal protein L19 /


Mass: 13619.865 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: D0CCR8
#16: Protein 50S ribosomal protein L20 /


Mass: 13468.946 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: D0CA76
#17: Protein 50S ribosomal protein L21 /


Mass: 11496.364 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: D0CDQ6
#18: Protein 50S ribosomal protein L22 /


Mass: 11960.126 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: D0CD02
#19: Protein 50S ribosomal protein L23 /


Mass: 11607.392 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: D0CCZ9
#20: Protein 50S ribosomal protein L24 /


Mass: 11187.929 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: D0CD08
#21: Protein 50S ribosomal protein L25 /


Mass: 10914.539 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: D0C9L7
#22: Protein 50S ribosomal protein L27 /


Mass: 9072.387 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: D0CDQ7
#23: Protein 50S ribosomal protein L28 /


Mass: 9125.756 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: D0CAL0
#24: Protein 50S ribosomal protein L29 /


Mass: 7449.678 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: D0CD05
#25: Protein 50S ribosomal protein L30 /


Mass: 6654.788 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: D0CD15
#26: Protein 50S ribosomal protein L32 /


Mass: 7096.888 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: D0C9K5
#27: Protein 50S ribosomal protein L33 /


Mass: 6105.310 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: D0CAL1
#28: Protein/peptide 50S ribosomal protein L34 /


Mass: 5192.247 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: D0CG06
#29: Protein 50S ribosomal protein L35 /


Mass: 7424.098 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: D0CA77
#30: Protein/peptide 50S ribosomal protein L36 /


Mass: 4276.201 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: D0CD18

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Non-polymers , 2 types, 161 molecules

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


Mass: 24.305 Da / Num. of mol.: 160 / Source method: obtained synthetically / Formula: Mg
#32: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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 - 50S subunit
Type: RIBOSOME / Entity ID: #1-#30 / 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
9RELION3initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
13PHENIX1.17.1-3660model refinement
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: 51958
Details: Multi-body refinement was carried out in RELION 3.0 to obtain the final '50S subunit' 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: 20.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007390840
ELECTRON MICROSCOPYf_angle_d0.7748136537
ELECTRON MICROSCOPYf_chiral_restr0.047117600
ELECTRON MICROSCOPYf_plane_restr0.00556899
ELECTRON MICROSCOPYf_dihedral_angle_d16.168236948

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