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- PDB-6v39: Cryo-EM structure of the Acinetobacter baumannii Ribosome: 70S wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6v39 | ||||||
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Title | Cryo-EM structure of the Acinetobacter baumannii Ribosome: 70S with P-site tRNA | ||||||
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![]() | RIBOSOME / Acinetobacter baumannii | ||||||
Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||
![]() | Morgan, C.E. / Yu, E.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development. Authors: Christopher E Morgan / Wei Huang / Susan D Rudin / Derek J Taylor / James E Kirby / Robert A Bonomo / Edward W Yu / ![]() Abstract: Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the ...Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections. is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21030MC ![]() 6v3aC ![]() 6v3bC ![]() 6v3dC ![]() 6v3eC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ
-RNA chain , 5 types, 5 molecules AN1BsN1vw
#5: RNA chain | Mass: 945299.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#6: RNA chain | Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: RNA chain | Mass: 500297.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: RNA chain | Mass: 24760.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#53: RNA chain | Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#32: Protein | Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#33: Protein | Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#34: Protein | Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA15 |
#35: Protein | Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA22 |
#36: Protein | Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IBC1 |
#37: Protein | Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7I7S0 |
#38: Protein | Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA25 |
#39: Protein | Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7I7R9 |
#43: Protein | Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA17 |
#44: Protein | Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA26 |
#45: Protein | Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7I3U0 |
#46: Protein | Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#47: Protein | Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA30 |
#48: Protein | Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7IA35 |
#50: Protein | Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: AB0057 / References: UniProt: B7I5N9 |
#51: Protein | Mass: 8474.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 5 types, 390 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FME.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#54: Chemical | ChemComp-ZN / | ||||
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#55: Chemical | ChemComp-FME / | ||||
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-NA / | #58: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Acinetobacter baumannii 70S ribosome with P-site tRNA / Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL |
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Molecular weight | Value: 2.3 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24306 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5AFI | ||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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