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- EMDB-1290: Lengsin is a survivor of an ancient family of class I glutamine s... -

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Basic information

Entry
Database: EMDB / ID: EMD-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.
Map dataLengsin
Sample
  • Sample: Lengsin
  • Protein or peptide: Lengsin
Function / homology
Function and homology information


glutamine biosynthetic process / glutamine synthetase activity / plasma membrane
Similarity search - Function
Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsWyatt K / White HE / Wang L / Bateman OA / Slingsby C / Orlova EV / Wistow G
CitationJournal: 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
DepositionNov 9, 2006-
Header (metadata) releaseNov 9, 2006-
Map releaseMar 20, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2j9i
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1290.gif

Downloads & links

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Map

FileDownload / File: emd_1290.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLengsin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 120 pix.
= 174. Å		1.45 Å/pix.
x 120 pix.
= 174. Å		1.45 Å/pix.
x 120 pix.
= 174. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.299 / Movie #1: 0.1
Minimum - Maximum-0.608063 - 0.900813
Average (Standard dev.)0.0221071 (±0.125035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 174 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-0.6080.9010.022

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Supplemental data

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Sample components

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Entire : Lengsin

EntireName: Lengsin
Components
  • Sample: Lengsin
  • Protein or peptide: Lengsin

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Supramolecule #1000: Lengsin

SupramoleculeName: Lengsin / type: sample / ID: 1000 / Oligomeric state: dodecamer / Number unique components: 1
Molecular weightExperimental: 510 KDa / Theoretical: 620.32 KDa

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Macromolecule #1: Lengsin

MacromoleculeName: 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 expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 6 / Details: 25 mM malonic acid
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
DetailsLow dose mode
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.32 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan single tilt negative stain holder / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: phase flipping
Final reconstructionApplied 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 classificationNumber classes: 150

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Atomic model buiding 1

Initial modelPDB ID:

1f52

SoftwareName: URO
DetailsProtocol: Rigid Body. The domains were docked manually using COOT
RefinementProtocol: RIGID BODY FIT
Output model

PDB-2j9i:
Lengsin is a survivor of an ancient family of class I glutamine synthetases in eukaryotes that has undergone evolutionary re- engineering for a tissue-specific role in the vertebrate eye lens.

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