+Open data
-Basic information
Entry | Database: PDB / ID: 6pew | |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM Plasmodium falciparum glutamine synthetase | |||||||||||||||||||||||||||||||||
Components | Glutamine synthetase | |||||||||||||||||||||||||||||||||
Keywords | LIGASE / glutamine synthetase | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||||||||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||||||||||||||
Authors | Ho, C.M. / Lai, M. / Zhou, Z.H. | |||||||||||||||||||||||||||||||||
Funding support | United States, 10items
| |||||||||||||||||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pew.cif.gz | 1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pew.ent.gz | 910.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/6pew ftp://data.pdbj.org/pub/pdb/validation_reports/pe/6pew | HTTPS FTP |
---|
-Related structure data
Related structure data | 20334MC 6pevC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 63309.551 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (isolate NF54) (eukaryote) Strain: isolate NF54 / References: UniProt: A0A2I0BT46, UniProt: W7JM41*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Plasmodium falciparum glutamine synthetase / Type: COMPLEX / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Plasmodium falciparum (isolate NF54) (eukaryote) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D6 (2x6 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8350 / Symmetry type: POINT |