+Open data
-Basic information
Entry | Database: PDB / ID: 8j1z | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The global structure of pre50S related to DbpA in state3 | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | RIBOSOME / pre50S / DbpA | ||||||||||||||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||||||||
Authors | Yu, T. / Zeng, F. | ||||||||||||||||||
Funding support | China, 5items
| ||||||||||||||||||
Citation | Journal: To Be Published Title: PTC Remodeling in Pre50S Intermediates: Insights into the Role of DEAD-box RNA Helicase DbpA Authors: Yu, T. / Jiang, J. / Yu, Q. / Li, X. / Dong, W. / Zeng, F. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8j1z.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8j1z.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 8j1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j1z_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8j1z_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8j1z_validation.xml.gz | 118.8 KB | Display | |
Data in CIF | 8j1z_validation.cif.gz | 214.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/8j1z ftp://data.pdbj.org/pub/pdb/validation_reports/j1/8j1z | HTTPS FTP |
-Related structure data
Related structure data | 35939MC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 2 types, 2 molecules ab
#1: RNA chain | Mass: 941725.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 42756 |
---|---|
#2: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1370526514 |
+50S ribosomal protein ... , 25 types, 25 molecules cdefijkmnopqrstuvwxyz012h
-Non-polymers , 2 types, 874 molecules
#28: Chemical | ChemComp-MG / #29: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ribosome 50S subunit / Type: RIBOSOME / Entity ID: #1-#27 / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 / Details: 20mM HEPES-KOH,pH7.5;140mM NH4Cl;10mM Mg2+,1mM DTT |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: DARK FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55280 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.09 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
|