[English] 日本語
Yorodumi- PDB-6v3d: Cryo-EM structure of the Acinetobacter baumannii Ribosome: 50S subunit -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v3d | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the Acinetobacter baumannii Ribosome: 50S subunit | ||||||
Components |
| ||||||
Keywords | RIBOSOME / Acinetobacter baumannii | ||||||
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 | ||||||
Biological species | Acinetobacter sp. CIP 51.11 (bacteria) Acinetobacter beijerinckii ANC 3835 (bacteria) Acinetobacter baumannii (bacteria) Acinetobacter sp. ANC 4470 (bacteria) Acinetobacter baumannii AB0057 (bacteria) Acinetobacter sp. NIPH 899 (bacteria) Acinetobacter sp. 809848 (bacteria) Acinetobacter rudis CIP 110305 (bacteria) Acinetobacter sp. CIP 102082 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | ||||||
Authors | Morgan, C.E. / Yu, E.W. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: mBio / Year: 2020 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6v3d.cif.gz | 2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6v3d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6v3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/6v3d ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v3d | HTTPS FTP |
---|
-Related structure data
Related structure data | 21033MC 6v39C 6v3aC 6v3bC 6v3eC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+50S ribosomal protein ... , 28 types, 28 molecules 0123CDEFGHIJKLMNOPQRSTUVWXYZ
-RNA chain , 2 types, 2 molecules AN1B
#5: RNA chain | Mass: 945299.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii AB0057 (bacteria) |
---|---|
#6: RNA chain | Mass: 36996.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: GenBank: 1360860747 |
-Non-polymers , 4 types, 339 molecules
#31: Chemical | ChemComp-ZN / | ||||
---|---|---|---|---|---|
#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-NA / | #34: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Acinetobacter baumannii Large Ribosomal Subunit / Type: RIBOSOME / Entity ID: #1-#30 / Source: NATURAL |
---|---|
Molecular weight | Value: 2.3 MDa / Experimental value: NO |
Source (natural) | Organism: Acinetobacter baumannii AB0057 (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27020 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5AFI Accession code: 5AFI / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|