[English] 日本語
Yorodumi
- EMDB-12589: Plasmodium falciparum Glutamine synthetase (PfGs) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12589
TitlePlasmodium falciparum Glutamine synthetase (PfGs)
Map data
Sample
  • Organelle or cellular component: P falciparum Glutamine synthetase
    • Protein or peptide: Glutamine synthetase
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.8 Å
AuthorsMakumire S / Mlelu AE / Gqunu S / Weber WB / Sewell BT
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: To Be Published
Title: The structure of glutamine synthetase from Plasmodium falciparum
Authors: Makumire S / Gqunu S / Mlelu AE / Weber WB / Sewell BT
History
DepositionMar 9, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateMar 23, 2022-
Current statusMar 23, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_12589.png

Downloads & links

-
Map

FileDownload / File: emd_12589.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.388
Minimum - Maximum-0.9200489 - 1.5392768
Average (Standard dev.)0.0133323725 (±0.08479103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_12589_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12589_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12589_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : P falciparum Glutamine synthetase

EntireName: P falciparum Glutamine synthetase
Components
  • Organelle or cellular component: P falciparum Glutamine synthetase
    • Protein or peptide: Glutamine synthetase

-
Supramolecule #1: P falciparum Glutamine synthetase

SupramoleculeName: P falciparum Glutamine synthetase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightExperimental: 756 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLIKLFFSNN AELYEYIKDK KNDVEIVACI ITNLLGTYFK CFFYVKEITL NKLESGFSFD ASSIKLCSD TEVSDFFIKV DHSTCYLEEC DGKNILNIMC DIKRYNGFDY YKCPRTILKK T CEFVKNEG IADKVCIGNE LEFFIFDKVN YSLDEYNTYL KVYDRESFSC ...String:
MLIKLFFSNN AELYEYIKDK KNDVEIVACI ITNLLGTYFK CFFYVKEITL NKLESGFSFD ASSIKLCSD TEVSDFFIKV DHSTCYLEEC DGKNILNIMC DIKRYNGFDY YKCPRTILKK T CEFVKNEG IADKVCIGNE LEFFIFDKVN YSLDEYNTYL KVYDRESFSC KNDLSSIYGN HV VNKVEPH KDHFNNPNNE YLINDDSKKV KKKSGYFTTD PYDTSNIIKL RICRALNDMN INV QRYHHE VSTSQHEISL KYFDALTNAD FLLITKQIIK TTVSSFNRTA TFMPKPLVND NGNG LHCNI SLWKNNKNIF YHNDPSTFFL SKESFYFMYG IVKHAKALQA FCNATMNSYK RLVPG FETC QKLFYSFGSR SAVIRLSLIN YSNPSEKRIE FRLPDCANSP HLVMAAIILA GYDGIK SKE QPLVPFESKD NHFYISSIFS KYVQHPENFN ILTHALEGYE SLHTINESPE FKNFFKC EE PQGISFSLVE SLDALEKDHA FLTVNNIFTE EMIQEYIKFK REEIDAYNKY VNAYDYHL Y YEC

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl acetate
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.34 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 180119
CTF correctionSoftware - Name: cryoSPARC (ver. 3.1.0)
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 180119
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC

-
Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL

+
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