+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20333 | |||||||||||||||||||||||||||||||||
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Title | CryoEM Plasmodium falciparum M18 aspartyl aminopeptidase | |||||||||||||||||||||||||||||||||
Map data | Plasmodium falciparum M18 | |||||||||||||||||||||||||||||||||
Sample |
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Function / homology | Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / aminopeptidase activity / metallopeptidase activity / zinc ion binding / M18 aspartyl aminopeptidase Function and homology information | |||||||||||||||||||||||||||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) / Plasmodium falciparum (isolate NF54) (eukaryote) | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||||||||||||||
Authors | Ho C / 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_20333.map.gz | 12.2 MB | EMDB map data format | |
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Header (meta data) | emd-20333-v30.xml emd-20333.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_20333.png | 83.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20333 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20333 | HTTPS FTP |
-Validation report
Summary document | emd_20333_validation.pdf.gz | 375.1 KB | Display | EMDB validaton report |
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Full document | emd_20333_full_validation.pdf.gz | 374.7 KB | Display | |
Data in XML | emd_20333_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_20333_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20333 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20333 | HTTPS FTP |
-Related structure data
Related structure data | 6pevMC 6pewC 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_20333.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Plasmodium falciparum M18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 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 M18 aspartyl aminopeptidase
Entire | Name: Plasmodium falciparum M18 aspartyl aminopeptidase |
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Components |
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-Supramolecule #1: Plasmodium falciparum M18 aspartyl aminopeptidase
Supramolecule | Name: Plasmodium falciparum M18 aspartyl aminopeptidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
-Macromolecule #1: M18 aspartyl aminopeptidase
Macromolecule | Name: M18 aspartyl aminopeptidase / 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: 65.72193 KDa |
Sequence | String: MDKKAREYAQ DALKFIQRSG SNFLACKNLK ERLENNGFIN LSEGETWNLN KNEGYVLCKE NRNICGFFVG KNFNIDTGSI LISIGHIDS CALKISPNNN VIKKKIHQIN VECYGSGLWH TWFDRSLGLS GQVLYKKGNK LVEKLIQINK SVLFLPSLAI H LQNRTRYD ...String: MDKKAREYAQ DALKFIQRSG SNFLACKNLK ERLENNGFIN LSEGETWNLN KNEGYVLCKE NRNICGFFVG KNFNIDTGSI LISIGHIDS CALKISPNNN VIKKKIHQIN VECYGSGLWH TWFDRSLGLS GQVLYKKGNK LVEKLIQINK SVLFLPSLAI H LQNRTRYD FSVKINYENH IKPIISTTLF NQLNKCKRNN VHHDTILTTD TKFSHKENSQ NKRDDQMCHS FNDKDVSNHN LD KNTIEHL TNQQNEEKNK HTKDNPNSKD IVEHINTDNS YPLLYLLSKE LNCKEEDILD FELCLMDTQE PCFTGVYEEF IEG ARFDNL LGSFCVFEGF IELVNSIKNH TSNENTNHTN NITNDINDNI HNNLYISIGY DHEEIGSLSE VGARSYCTKN FIDR IISSV FKKEIHEKNL SVQEIYGNLV NRSFILNVDM AHCSHPNYPE TVQDNHQLFF HEGIAIKYNT NKNYVTSPLH ASLIK RTFE LYYNKYKQQI KYQNFMVKND TPCGSTVGSM VAANLSMPGI DIGIPQLAMH SIREIAAVHD VFFLIKGVFA FYTYYN QVL STCVHDK |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-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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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: cryoSPARC (ver. 1) |
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Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1) / Number images used: 5860 |
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 1) |
Final angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 1) |