+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32509 | |||||||||
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Title | Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase | |||||||||
Map data | Apo LdGDP-MP | |||||||||
Sample |
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Keywords | protozoan enzyme / Leishmania donovani / SUGAR BINDING PROTEIN | |||||||||
Function / homology | Function and homology information mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / GTP binding Similarity search - Function | |||||||||
Biological species | Leishmania donovani (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Xu W / Li H / Huang C | |||||||||
Funding support | China, 2 items
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Citation | Journal: Cell Discov / Year: 2022 Title: Structural insights into selective inhibition of leishmanial GDP-mannose pyrophosphorylase. Authors: Hang Li / Tuo Ji / Qi Sun / Yao Chen / Weiya Xu / Chengdong Huang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32509.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-32509-v30.xml emd-32509.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_32509.png | 80.6 KB | ||
Filedesc metadata | emd-32509.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32509 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32509 | HTTPS FTP |
-Validation report
Summary document | emd_32509_validation.pdf.gz | 487.2 KB | Display | EMDB validaton report |
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Full document | emd_32509_full_validation.pdf.gz | 486.8 KB | Display | |
Data in XML | emd_32509_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_32509_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32509 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32509 | HTTPS FTP |
-Related structure data
Related structure data | 7whrMC 7whsC 7whtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32509.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Apo LdGDP-MP | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.01 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Ld GDP-MP
Entire | Name: Ld GDP-MP |
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Components |
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-Supramolecule #1: Ld GDP-MP
Supramolecule | Name: Ld GDP-MP / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Leishmania donovani (eukaryote) |
-Macromolecule #1: Nucleotidyl transferase family protein
Macromolecule | Name: Nucleotidyl transferase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Leishmania donovani (eukaryote) |
Molecular weight | Theoretical: 41.780074 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSASDGQGMR AVILVGGFGT RLRPLTLTTP KPLVPFCNKP MIIHQIEALK AVGVTEVILA VAYRPEAMKE QMDEWSRKLG VSFVFSVEE EPLGTAGPLA LARDILMQDD KPFFVLNSDV TCTFPMQELL DFHKAHGGEG TIMVSQVTQW EKYGVVVYSP Q NYQIERFV ...String: MSASDGQGMR AVILVGGFGT RLRPLTLTTP KPLVPFCNKP MIIHQIEALK AVGVTEVILA VAYRPEAMKE QMDEWSRKLG VSFVFSVEE EPLGTAGPLA LARDILMQDD KPFFVLNSDV TCTFPMQELL DFHKAHGGEG TIMVSQVTQW EKYGVVVYSP Q NYQIERFV EKPSRFLGDR INAGIYIFNK SILDRIPPRR ASIEKEIFPA MAAEGQLYAF NLEGFWMDVG QPKDYILGMT KF IPSLVHG NRETEQLHTE AVEHQRGGRF TVIGASLIDP SAKIGDGAVI GPYASIGANC VIGESCRIDN AAILENSKVG KGT MVSRSI VGWNNRIGSW CHIKDISVLG DDVEVKDGVI LIGTKVLPNK DVGEHRFEPG IIM UniProtKB: mannose-1-phosphate guanylyltransferase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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) / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56825 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |