+Open data
-Basic information
Entry | Database: PDB / ID: 8kab | |||||||||
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Title | Mycobacterium smegmatis 50S ribosomal subunit-HflX complex | |||||||||
Components |
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Keywords | RIBOSOME / Complex | |||||||||
Function / homology | Function and homology information large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation ...large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Srinivasan, K. / Banerjee, A. / Sengupta, J. | |||||||||
Funding support | India, 2items
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Citation | Journal: Structure / Year: 2024 Title: Cryo-EM structures reveal the molecular mechanism of HflX-mediated erythromycin resistance in mycobacteria. Authors: Krishnamoorthi Srinivasan / Aneek Banerjee / Jayati Sengupta / Abstract: Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. ...Mycobacterial HflX confers resistance against macrolide antibiotics. However, the exact molecular mechanism is poorly understood. To gain further insights, we determined the cryo-EM structures of M. smegmatis (Msm) HflX-50S subunit and 50S subunit-erythromycin (ERY) complexes at a global resolution of approximately 3 Å. A conserved nucleotide A2286 at the gate of nascent peptide exit tunnel (NPET) adopts a swayed conformation in HflX-50S complex and interacts with a loop within the linker helical (LH) domain of MsmHflX that contains an additional 9 residues insertion. Interestingly, the swaying of this nucleotide, which is usually found in the non-swayed conformation, is induced by erythromycin binding. Furthermore, we observed that erythromycin decreases HflX's ribosome-dependent GTP hydrolysis, resulting in its enhanced binding and anti-association activity on the 50S subunit. Our findings reveal how mycobacterial HflX senses the presence of macrolides at the peptide tunnel entrance and confers antibiotic resistance in mycobacteria. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kab.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8kab.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8kab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/8kab ftp://data.pdbj.org/pub/pdb/validation_reports/ka/8kab | HTTPS FTP |
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-Related structure data
Related structure data | 37007MC 8xz3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 32 types, 32 molecules 3CDEFGHIJKLMNOPQRSTUVWXYZabcdefg
-RNA chain , 2 types, 2 molecules AB
#2: RNA chain | Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: GenBank: 118168627 |
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#3: RNA chain | Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: GenBank: 118168627 |
-Protein / Non-polymers , 2 types, 2 molecules h
#35: Protein | Mass: 52163.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: hflX / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0QVY1 |
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#36: Chemical | ChemComp-GNP / |
-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
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Source (natural) |
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Source (recombinant) |
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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 defocus max: 3300 nm / Nominal defocus min: 1800 nm |
Image recording | Electron dose: 28.26 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121211 / Symmetry type: POINT |