+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20334 | |||||||||||||||||||||||||||||||||
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Title | CryoEM Plasmodium falciparum glutamine synthetase | |||||||||||||||||||||||||||||||||
Map data | Plasmodium falciparum glutamine synthetase | |||||||||||||||||||||||||||||||||
Sample |
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Keywords | glutamine synthetase / LIGASE | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||||||||||||||
Biological species | Plasmodium falciparum (isolate NF54) (eukaryote) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||||||||||||||
Authors | Ho CM / Zhou ZH | |||||||||||||||||||||||||||||||||
Funding support | United States, 10 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20334.map.gz | 13.6 MB | EMDB map data format | |
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Header (meta data) | emd-20334-v30.xml emd-20334.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_20334.png | 86.7 KB | ||
Filedesc metadata | emd-20334.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20334 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20334 | HTTPS FTP |
-Related structure data
Related structure data | 6pewMC 6pevC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_20334.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Plasmodium falciparum glutamine synthetase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Plasmodium falciparum glutamine synthetase
Entire | Name: Plasmodium falciparum glutamine synthetase |
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Components |
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-Supramolecule #1: Plasmodium falciparum glutamine synthetase
Supramolecule | Name: Plasmodium falciparum glutamine synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Plasmodium falciparum (isolate NF54) (eukaryote) |
-Macromolecule #1: Glutamine synthetase
Macromolecule | Name: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Plasmodium falciparum (isolate NF54) (eukaryote) / Strain: isolate NF54 |
Molecular weight | Theoretical: 63.309551 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 recording | Film 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 |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 1) |
Final angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 1) |
Final reconstruction | Applied 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 |