[English] 日本語
Yorodumi- PDB-6ys8: Structure of GldLM, the proton-powered motor that drives protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ys8 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of GldLM, the proton-powered motor that drives protein transport and gliding motility | ||||||||||||
Components |
| ||||||||||||
Keywords | MOTOR PROTEIN / membrane protein complex ion-driven motor | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Flavobacterium johnsoniae (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Hennell James, R. / Deme, J.C. / Lea, S.M. | ||||||||||||
Funding support | United Kingdom, 3items
| ||||||||||||
Citation | Journal: Nat Microbiol / Year: 2020 Title: Structure of a proton-powered molecular motor that drives protein transport and gliding motility Authors: Hennell James, R. / Deme, J.C. / Kjaer, A. / Alcock, F. / Silale, A. / Lauber, F. / Bersk, B.C. / Lea, S.M. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ys8.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ys8.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ys8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/6ys8 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/6ys8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 10893MC 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: 54856.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: gldM / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EGM3 #2: Protein | Mass: 22786.209 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: gldL, SAMN05444388_10142 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EGM4 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GldLM / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Flavobacterium johnsoniae (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||
Buffer component |
| ||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / 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 / Nominal magnification: 165000 X / Nominal defocus max: 0.3 nm / Nominal defocus min: 0.1 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3284887 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119230 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |