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Yorodumi- PDB-6ytf: Acinetobacter baumannii ribosome-tigecycline complex - 30S subuni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ytf | |||||||||
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Title | Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head | |||||||||
Components |
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Keywords | RIBOSOME / antibiotic / tigecycline / translation | |||||||||
Function / homology | Function and homology information ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Nicholson, D. / Edwards, T.A. / O'Neill, A.J. / Ranson, N.A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ytf.cif.gz | 417.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ytf.ent.gz | 303.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ytf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ytf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ytf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ytf_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 6ytf_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6ytf ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6ytf | HTTPS FTP |
-Related structure data
Related structure data | 10915MC 6yhsC 6ypuC 6ys5C 6ysiC 6yt9C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10407 (Title: Motion-corrected micrographs and extracted particle images of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with tigecycline Data size: 538.5 Data #1: Motion-corrected micrographs of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with tigecycline [micrographs - single frame] Data #2: Extracted particle images of the 70S ribosome from the human pathogen Acinetobacter baumannii in complex with tigecycline [picked particles - multiframe - processed]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules 379
#1: RNA chain | Mass: 500126.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: GenBank: 692328596 |
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#2: RNA chain | Mass: 24818.893 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 (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) |
#3: RNA chain | 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 (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) |
-30S ribosomal protein ... , 7 types, 7 molecules dhjknot
#4: Protein | Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0CD03 |
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#5: Protein | 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 (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0C9P7 |
#6: Protein | Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0CG36 |
#7: Protein | Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0CCZ6 |
#8: Protein | Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0CD19 |
#9: Protein | Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0CD10 |
#10: Protein | Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) References: UniProt: D0CD01 |
-Non-polymers , 2 types, 25 molecules
#11: Chemical | ChemComp-MG / #12: Chemical | ChemComp-T1C / | |
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-Details
Has ligand of interest | Y |
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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 |
-Sample preparation
Component | Name: Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit head Type: RIBOSOME / Entity ID: #1-#10 / Source: NATURAL |
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Source (natural) | Organism: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria) |
Buffer solution | pH: 7.5 |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm |
Image recording | Average exposure time: 1.1 sec. / Electron dose: 62 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Movie frames/image: 50 |
-Processing
Software |
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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 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 head' reconstruction. The mask used for this procedure is deposited with this entry. Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient Details: The quality of the map is relatively poor so the related PDB entry 6YS5 (A. baumannii ribosome-amikacin complex - 30S subunit head) was rigid body fitted into the map using Chimera X-0.9, ...Details: The quality of the map is relatively poor so the related PDB entry 6YS5 (A. baumannii ribosome-amikacin complex - 30S subunit head) was rigid body fitted into the map using Chimera X-0.9, tigecycline was placed into the density at the primary site, and one round of global real space refinement and local refinement were carried out using PHENIX and Coot respectively, using ligand restraints in both cases. | ||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.23 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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