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Open data
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Basic information
Entry | Database: PDB / ID: 7mt3 | |||||||||
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Title | Mtb 70S with P/E tRNA | |||||||||
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![]() | RIBOSOME / Mycobacterium tuberculosis / ABCF ribosome complex / Antibiotic | |||||||||
Function / homology | ![]() peptidoglycan-based cell wall / large ribosomal subunit / regulation of translation / 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 ...peptidoglycan-based cell wall / large ribosomal subunit / regulation of translation / 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 / response to antibiotic / mRNA binding / RNA binding / zinc ion binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Cui, Z. / Zhang, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis. Authors: Zhicheng Cui / Xiaojun Li / Joonyoung Shin / Howard Gamper / Ya-Ming Hou / James C Sacchettini / Junjie Zhang / ![]() Abstract: EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited ...EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited due to the lack of high-resolution structures along its ATPase cycle. Here we present the cryo-electron microscopy (cryo-EM) structures of EttA from Mycobacterium tuberculosis (Mtb), referred to as MtbEttA, in complex with the Mtb 70S ribosome initiation complex (70SIC) at the pre-hydrolysis (ADPNP) and transition (ADP-VO) states, and the crystal structure of MtbEttA alone in the post-hydrolysis (ADP) state. We observe that MtbEttA binds the E-site of the Mtb 70SIC, remodeling the P-site tRNA and the ribosomal intersubunit bridge B7a during the ribosomal ratcheting. In return, the rotation of the 30S causes conformational changes in MtbEttA, forcing the two nucleotide-binding sites (NBSs) to alternate to engage each ADPNP in the pre-hydrolysis states, followed by complete engagements of both ADP-VO molecules in the ATP-hydrolysis transition states. In the post-hydrolysis state, the conserved ATP-hydrolysis motifs of MtbEttA dissociate from both ADP molecules, leaving two nucleotide-binding domains (NBDs) in an open conformation. These structures reveal a dynamic interplay between MtbEttA and the Mtb ribosome, providing insights into the mechanism of translational regulation by EttA-like proteins. | |||||||||
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 | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 23975MC ![]() 7mscC ![]() 7mshC ![]() 7msmC ![]() 7mszC ![]() 7mt2C ![]() 7mt7C ![]() 7mu0C C: citing same article ( M: map data used to model this data |
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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 ... , 31 types, 31 molecules 01234678CDEFGHJKLMNOPQRSTUVWXYZ
-RNA chain , 5 types, 5 molecules ABayz
#9: RNA chain | Mass: 1017820.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: GenBank: 1251771536 |
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#10: RNA chain | Mass: 37097.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: GenBank: 1251771551 |
#34: RNA chain | Mass: 498401.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: GenBank: 1464449751 |
#53: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#54: RNA chain | Mass: 8470.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-30S ribosomal protein ... , 18 types, 18 molecules cdefghijklmnopqrst
#35: Protein | Mass: 30071.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH37 |
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#36: Protein | Mass: 23515.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH35 |
#37: Protein | Mass: 22925.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH33 |
#38: Protein | Mass: 10952.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH31 |
#39: Protein | Mass: 17633.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH29 |
#40: Protein | Mass: 14432.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH27 |
#41: Protein | Mass: 16465.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH25 |
#42: Protein | Mass: 11452.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH67 |
#43: Protein | Mass: 14815.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH65 |
#44: Protein | Mass: 13882.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH63 |
#45: Protein | Mass: 14383.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH61 |
#46: Protein | Mass: 6841.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH57 |
#47: Protein | Mass: 10500.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH55 |
#48: Protein | Mass: 17466.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH53 |
#49: Protein | Mass: 14776.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH51 |
#50: Protein | Mass: 9565.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH49 |
#51: Protein | Mass: 10830.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH45 |
#52: Protein | Mass: 9428.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 25618 / H37Rv / References: UniProt: P9WH41 |
-Non-polymers , 2 types, 441 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#55: Chemical | ChemComp-ZN / #56: Chemical | ChemComp-MG / |
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-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: Mtb 70S with P/E tRNA / Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) |
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Buffer solution | pH: 7.5 | ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid type: Quantifoil R2/1 | ||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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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 / Cs: 2.7 mm |
Image recording | Electron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||
Particle selection | Num. of particles selected: 8949 | ||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134676 / Symmetry type: POINT |