+Open data
-Basic information
Entry | Database: PDB / ID: 6u5z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of E. coli LonA S679A | |||||||||
Components | Lon proteaseLon protease family | |||||||||
Keywords | HYDROLASE / Lon protease / hexamer | |||||||||
Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity ...endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / DNA binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Botos, I. / Lountos, G.T. / Weimin, W. / Wlodawer, A. | |||||||||
Funding support | United States, Russian Federation, 2items
| |||||||||
Citation | Journal: Curr Res Struct Biol / Year: 2020 Title: Cryo-EM structure of substrate-free E. coli Lon protease provides insights into the dynamics of Lon machinery Authors: Botos, I. / Lountos, G.T. / Weimin, W. / Cherry, S. / Ghirlando, R. / Kudzhaev, A.M. / Rotanova, T.V. / de Val, N. / Tropea, J. / Gustchina, A. / Wlodawer, A. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6u5z.cif.gz | 540.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6u5z.ent.gz | 455.1 KB | Display | PDB format |
PDBx/mmJSON format | 6u5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/6u5z ftp://data.pdbj.org/pub/pdb/validation_reports/u5/6u5z | HTTPS FTP |
---|
-Related structure data
Related structure data | 20659MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 87546.266 Da / Num. of mol.: 6 / Mutation: S679A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: lon, ACN002_0456, CV83915_01127, ECs0493, EL75_3311, EL80_3360 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: C3TLS2, UniProt: P0A9M0*PLUS, endopeptidase La |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: ATP-dependent protease LaEndopeptidase La / Type: COMPLEX / Details: S679A mutant / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.087 MDa / Experimental value: YES |
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 889189 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274765 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|