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Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens.

by single particle reconstruction, at 17 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.1, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.1, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2j9i, Surface level: 0.1, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1290
TitleLengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens.
MapLengsin
SampleLengsin
AuthorsWyatt K, White HE, Wang L, Bateman OA, Slingsby C, Orlova EV, Wistow G
DateDeposition: 2006-11-09, Header release: 2006-11-09, Map release: 2007-03-20, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.1, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.1, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2j9i, Surface level: 0.1, Made by UCSF CHIMERA

Supplemental images

1290.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-2j9i
CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)

Diagram

EMDB-2038

EMDB-1193

PDB-4a8a
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleStructure, Vol. 14, Issue 12, Page 1823-34, Year 2006
TitleLengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens.
AuthorsKeith Wyatt, Helen E White, Luchun Wang, Orval A Bateman, Christine Slingsby, Elena V Orlova, Graeme Wistow
Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
KeywordsAmino Acid Sequence, Animals, Catalysis, Cryoelectron Microscopy, Evolution, Molecular, Eye Proteins (metabolism), Glutamate-Ammonia Ligase (chemistry, 6.3.1.2), Humans, LGSN protein, human (6.3.1.2), Lens, Crystalline (metabolism), Mice, Molecular Sequence Data, Protein Structure, Tertiary, Rats, Sea Urchins, Sequence Homology, Amino Acid
LinksPII: S0969-2126(06)00435-7, DOI: 10.1016/j.str.2006.10.008, PubMed: 17161372, PMC: PMC1868402
Map
FileEMD-1290.map ( map file in CCP4 format, 6913 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.299, 0.1 (movie #1):
Minimum - Maximum: -0.608063 - 0.900813
Average (Standard dev.): 0.0221071 (0.125035)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin-60-60-60
Limit595959
Spacing120120120
Unit CellA= B= C: 174 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.45 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.451.451.45
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z174.000174.000174.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.6080.9010.022
Annotation DetailsLengsin
Supplement
Images
Images

1290.gif
Sample
NameLengsin
Oligomeric Statedodecamer
Number of Components1
Experimental Mass0.51MDa
Theoretical Mass0.62032MDa
Component #1: protein - Lengsin
Scientific nameLengsin
Oligomeric Detailsdodecamer
Number of Copies1
Scientific Name of SpeciesMus musculus

Common Name of Speciesmouse
NCBI taxonomy10090
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc0.3 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 25 mM malonic acid
pH: 6
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeFEI TECNAI 20
DetailsLow dose mode
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Imaging ModeBRIGHT FIELD
Defocus170 nm - 320 nm
Specimen Holder
HolderGatan single tilt negative stain holder
ModelOTHER
Camera
DetectorKodak SO163 film
Image Acquisition
Sampling Size7
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmexact-filter back projection
SoftwareIMAGIC
CTF Correctionphase flipping
Resolution By Author17 A
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Class Averages150
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
SoftwareURO
DetailsProtocol: Rigid Body. The domains were docked manually using COOT
PDB Entry ID1F52

PDB-1f52
Fitted Coordinate
PDB entry ID

PDB-2j9i
Download
Data from EMDB
Header (meta data in XML format)emd-1290.xml (6.8 KB)
Map dataemd_1290.map.gz (2.7 MB)
Images1290.gif (18.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1290
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.3 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 3.4 MB