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- EMDB-20334: CryoEM Plasmodium falciparum glutamine synthetase -

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Basic information

Entry
Database: EMDB / ID: EMD-20334
TitleCryoEM Plasmodium falciparum glutamine synthetase
Map dataPlasmodium falciparum glutamine synthetase
Sample
  • Complex: Plasmodium falciparum glutamine synthetase
    • Protein or peptide: Glutamine synthetase
Keywordsglutamine synthetase / LIGASE
Function / homology
Function and homology information


glutamine biosynthetic process / glutamine synthetase activity
Similarity search - Function
Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase / Glutamine synthetase, type I
Similarity search - Component
Biological speciesPlasmodium falciparum (isolate NF54) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHo CM / Zhou ZH
Funding support United States, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM071940 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)AI094386 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)DE025567 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR23057 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD018111 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)U24GM116792 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI007323 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99/R00 HL133453 United States
CitationJournal: Nat Methods / Year: 2020
Title: Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu.
Authors: Chi-Min Ho / Xiaorun Li / Mason Lai / Thomas C Terwilliger / Josh R Beck / James Wohlschlegel / Daniel E Goldberg / Anthony W P Fitzpatrick / Z Hong Zhou /
Abstract: X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up ...X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.
History
DepositionJun 21, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseDec 11, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pew
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20334.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium falciparum glutamine synthetase
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0557 / Movie #1: 0.0557
Minimum - Maximum-0.18051884 - 0.30449316
Average (Standard dev.)0.0005976254 (±0.010147204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z342.400342.400342.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1810.3040.001

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Supplemental data

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Sample components

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Entire : Plasmodium falciparum glutamine synthetase

EntireName: Plasmodium falciparum glutamine synthetase
Components
  • Complex: Plasmodium falciparum glutamine synthetase
    • Protein or peptide: Glutamine synthetase

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Supramolecule #1: Plasmodium falciparum glutamine synthetase

SupramoleculeName: Plasmodium falciparum glutamine synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium falciparum (isolate NF54) (eukaryote)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (isolate NF54) (eukaryote) / Strain: isolate NF54
Molecular weightTheoretical: 63.309551 KDa
SequenceString: MKSVSFSNNA ELYEYIKDKK NDVEIVACII TNLLGTYFKC FFYVKEITLN KLESGFSFDA SSIKLCSDTE VSDFFIKVDH STCYLEECD GKNILNIMCD IKRYNGFDYY KCPRTILKKT CEFVKNEGIA DKVCIGNELE FFIFDKVNYS LDEYNTYLKV Y DRESFSCK ...String:
MKSVSFSNNA ELYEYIKDKK NDVEIVACII TNLLGTYFKC FFYVKEITLN KLESGFSFDA SSIKLCSDTE VSDFFIKVDH STCYLEECD GKNILNIMCD IKRYNGFDYY KCPRTILKKT CEFVKNEGIA DKVCIGNELE FFIFDKVNYS LDEYNTYLKV Y DRESFSCK NDLSSIYGNH VVNKVEPHKD HFNNPNNEYL INDDSKKVKK KSGYFTTDPY DTSNIIKLRI CRALNDMNIN VQ RYHHEVS TSQHEISLKY FDALTNADFL LITKQIIKTT VSSFNRTATF MPKPLVNDNG NGLHCNISLW KNNKNIFYHN DPS TFFLSK ESFYFMYGIV KHAKALQAFC NATMNSYKRL VPGFETCQKL FYSFGSRSAV IRLSLINYSN PSEKRIEFRL PDCA NSPHL VMAAIILAGY DGIKSKEQPL VPFESKDNHF YISSIFSKYV QHPENFNILT HALEGYESLH TINESPEFKN FFKCE EPQG ISFSLVESLD ALEKDHAFLT VNNIFTEEMI QEYIKFKREE IDAYNKYVNA YDYHLYYEC

UniProtKB: Glutamine synthetase

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 1)
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Number images used: 8350

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