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Open data
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Basic information
Entry | Database: PDB / ID: 9dyg | |||||||||
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Title | iSAT-PNA-RA20, RA20-B-c class | |||||||||
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![]() | RIBOSOME / 50S subunit / assembly intermediate / RNA-protein complex | |||||||||
Function / homology | ![]() transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / DNA-templated transcription termination / mRNA 5'-UTR binding ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / translation repressor activity / assembly of large subunit precursor of preribosome / ribosome assembly / cytosolic ribosome assembly / DNA-templated transcription termination / mRNA 5'-UTR binding / large ribosomal subunit / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.27 Å | |||||||||
![]() | Sheng, K. / Dong, X. / Lee, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Domain consolidation in bacterial 50S assembly revealed by anti-sense oligonucleotide probing Authors: Sheng, K. / Dong, X. / Aiyer, S. / Lee, J. / Djordjevic-Marquardt, S. / Lyumkis, D. / Williamson, J.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 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 | ![]() 47303MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-RNA chain , 1 types, 1 molecules CA
#1: RNA chain | Mass: 565405.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Large ribosomal subunit protein ... , 13 types, 13 molecules 2DEJKNPQRSTUY
#2: Protein/peptide | Mass: 4290.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 21763.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 12080.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 13721.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 12941.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 10546.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 11078.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Details
Has ligand of interest | N |
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Has protein modification | N |
-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: iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate Type: RIBOSOME / Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: Most of the sucrose was removed by spin concentration. | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Au-flat 1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K / Details: 3 microliter of the sample was added. |
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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 / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2 sec. / Electron dose: 25.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 |
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Processing
EM software |
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CTF correction | Details: CTF correction were performed by Patch CTF Estimation of cryoSPARC Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 120.42 / Protocol: OTHER / Space: REAL / Target criteria: Comprehensive validation (cryo-EM) Details: The atomic model was fitted into a low resolution (5 Angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. ...Details: The atomic model was fitted into a low resolution (5 Angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. Initial docking of the atomic model was done in ChimeraX. Coot and Phenix were used for real-space refinements. Geometry minimization in Phenix was used to improve the RNA atomic model. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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