[English] 日本語
Yorodumi
- EMDB-1204: Three-dimensional structure of a type III glutamine synthetase by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1204
TitleThree-dimensional structure of a type III glutamine synthetase by single-particle reconstruction.
Map dataGlutamine synthetase type III from Bacteroides fragilis
Sample
  • Sample: B.fragilis GlnN purified from E.coli
  • Protein or peptide: GlnN
Function / homologyGlutamine synthetase, N-terminal domain
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.0 Å
Authorsvan Rooyen JM / Abratt VR / Sewell BT
CitationJournal: J Mol Biol / Year: 2006
Title: Three-dimensional structure of a type III glutamine synthetase by single-particle reconstruction.
Authors: Jason M van Rooyen / Valerie R Abratt / B Trevor Sewell /
Abstract: GlnN, the type III glutamine synthetase (GSIII) from the medically important, anaerobic, opportunistic pathogen Bacteroides fragilis, has 82.8 kDa subunits that share only 9% sequence identity with ...GlnN, the type III glutamine synthetase (GSIII) from the medically important, anaerobic, opportunistic pathogen Bacteroides fragilis, has 82.8 kDa subunits that share only 9% sequence identity with the type I glutamine synthetases (GSI), the only family for which a structure is known. Active GlnN was found predominantly in a single peak that eluted from a calibrated gel-filtration chromatography column at a position equaivalent to 0.86(+/-0.08) MDa. Negative-stain electron microscopy enabled the identification of double-ringed particles and single hexameric rings ("pinwheels") resulting from partial staining. A 2D average of these pinwheels showed marked similarity to the corresponding structures found in preparations of GSI, except that the arms of the subunits were 40% longer. Reconstructions from particles embedded in vitreous ice showed that GlnN has a double-ringed, dodecameric structure with a 6-fold dihedral space group (D6) symmetry and dimensions of 17.0 nm parallel with the 6-fold axis and 18.3 nm parallel with the 2-fold axes. The structures, combined with a sequence alignment based on structural principles, showed how many aspects of the structure of GSI, and most notably the alpha/beta barrel fold active site were preserved. There was evidence for the presence of this structure in the reconstructed volume, thus, identifying the indentations between the pinwheel spokes as putative active sites and suggesting conservation of the overall molecular geometry found in GSI despite their low level of global homology. Furthermore, docking of GSI into the reconstruction left sufficient plausibly located unoccupied density to account for the additional residues in GSIII, thus validating the structure.
History
DepositionMar 20, 2006-
Header (metadata) releaseMar 20, 2006-
Map releaseAug 9, 2006-
UpdateFeb 21, 2012-
Current statusFeb 21, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1204.gif

Downloads & links

-
Map

FileDownload / File: emd_1204.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlutamine synthetase type III from Bacteroides fragilis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 90 pix.
= 360. Å		4 Å/pix.
x 90 pix.
= 360. Å		4 Å/pix.
x 90 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0163 / Movie #1: 0.05
Minimum - Maximum-0.188402 - 0.14922
Average (Standard dev.)0.000408487 (±0.0159002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions909090
Spacing909090
CellA=B=C: 360 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-0.1880.1490.000

-
Supplemental data

-
Sample components

-
Entire : B.fragilis GlnN purified from E.coli

EntireName: B.fragilis GlnN purified from E.coli
Components
  • Sample: B.fragilis GlnN purified from E.coli
  • Protein or peptide: GlnN

-
Supramolecule #1000: B.fragilis GlnN purified from E.coli

SupramoleculeName: B.fragilis GlnN purified from E.coli / type: sample / ID: 1000 / Oligomeric state: One dodecamer of GlnN / Number unique components: 1
Molecular weightExperimental: 1.3 MDa / Theoretical: 990 KDa / Method: Calibrated gel-filtration

-
Macromolecule #1: GlnN

MacromoleculeName: GlnN / type: protein_or_peptide / ID: 1 / Name.synonym: GSIII
Details: Recombinant GlnN purified from GlnA deficient E.coli mutant
Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Organism: Bacteroides fragilis (bacteria) / Strain: B. fragilis BF-1 / Tissue: E.coli cytoplasm / Cell: E.coli
Molecular weightExperimental: 990 KDa / Theoretical: 1.3 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pJS139
SequenceInterPro: Glutamine synthetase, N-terminal domain

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.15 / Details: 10 mM Imidazole-HCl, 10 mM MnCl2
StainingType: NEGATIVE / Details: cryo-EM
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: EMBL-designed plunger. Vitrification carried out in humidified room.
Method: Blot for 2 seconds before

-
Electron microscopy

MicroscopeFEI TECNAI 20
TemperatureAverage: 77 K
DateApr 26, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 14 µm / Number real images: 53
Details: Images were digitized using an Ilford Leafscan and downsized by a factor of 14 (as above) to give a sampling of 4 Å/pixel
Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.47 µm / Nominal defocus min: 1.01 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: Phase flipping of particles in defocus groups
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 15688
Final two d classificationNumber classes: 120

-
Atomic model buiding 1

SoftwareName: Situs
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: CC score

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more