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- EMDB-32511: Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in... -
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Open data
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Basic information
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Title | Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in complex with GDP-Mannose | |||||||||
![]() | Ld GDP-MP with GDP-Mannose | |||||||||
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![]() | protozoan enzyme / Leishmania donovani / SUGAR BINDING PROTEIN | |||||||||
Function / homology | ![]() mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / protein glycosylation / GTP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Xu W / Li H / Huang C | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
Images | ![]() | 93.2 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7whtMC ![]() 7whrC ![]() 7whsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Ld GDP-MP with GDP-Mannose | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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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: #1 |
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Source (natural) | Organism: ![]() |
-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: ![]() |
Molecular weight | Theoretical: 41.780074 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
-Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / type: ligand / ID: 2 / Number of copies: 6 / Formula: GDD |
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Molecular weight | Theoretical: 605.341 Da |
Chemical component information | ![]() ChemComp-GDD: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123461 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |