[English] 日本語
Yorodumi- EMDB-1290: Lengsin is a survivor of an ancient family of class I glutamine s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1290 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. | |||||||||
Map data | Lengsin | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 17.0 Å | |||||||||
Authors | Wyatt K / White HE / Wang L / Bateman OA / Slingsby C / Orlova EV / Wistow G | |||||||||
Citation | Journal: Structure / Year: 2006 Title: Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. Authors: Keith Wyatt / Helen E White / Luchun Wang / Orval A Bateman / Christine Slingsby / Elena V Orlova / Graeme Wistow / Abstract: Lengsin is a major protein of the vertebrate eye lens. It belongs to the hitherto purely prokaryotic GS I branch of the glutamine synthetase (GS) superfamily, but has no enzyme activity. Like the ...Lengsin is a major protein of the vertebrate eye lens. It belongs to the hitherto purely prokaryotic GS I branch of the glutamine synthetase (GS) superfamily, but has no enzyme activity. Like the taxon-specific crystallins, Lengsin is the result of the recruitment of an ancient enzyme to a noncatalytic role in the vertebrate lens. Cryo-EM and modeling studies of Lengsin show a dodecamer structure with important similarities and differences with prokaryotic GS I structures. GS homology regions of Lengsin are well conserved, but the N-terminal domain shows evidence of dynamic evolutionary changes. Compared with birds and fish, most mammals have an additional exon corresponding to part of the N-terminal domain; however, in human, this is a nonfunctional pseudoexon. Genes related to Lengsin are also present in the sea urchin, suggesting that this branch of the GS I family, supplanted by GS II enzymes in vertebrates, has an ancient role in metazoans. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1290.map.gz | 2.7 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1290-v30.xml emd-1290.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | 1290.gif | 18.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1290 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1290 | HTTPS FTP |
-Validation report
Summary document | emd_1290_validation.pdf.gz | 230.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1290_full_validation.pdf.gz | 229.6 KB | Display | |
Data in XML | emd_1290_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1290 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1290 | HTTPS FTP |
-Related structure data
Related structure data | 2j9iMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_1290.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Lengsin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Lengsin
Entire | Name: Lengsin |
---|---|
Components |
|
-Supramolecule #1000: Lengsin
Supramolecule | Name: Lengsin / type: sample / ID: 1000 / Oligomeric state: dodecamer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 510 KDa / Theoretical: 620.32 KDa |
-Macromolecule #1: Lengsin
Macromolecule | Name: Lengsin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: dodecamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) / synonym: mouse |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
---|---|
Buffer | pH: 6 / Details: 25 mM malonic acid |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI 20 |
---|---|
Details | Low dose mode |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.32 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan single tilt negative stain holder / Specimen holder model: OTHER |
-Image processing
CTF correction | Details: phase flipping |
---|---|
Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC |
Final two d classification | Number classes: 150 |
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Software | Name: URO |
Details | Protocol: Rigid Body. The domains were docked manually using COOT |
Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-2j9i: |