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- EMDB-32510: Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in... -

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Basic information

Entry
Database: EMDB / ID: EMD-32510
TitleCryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in complex with GTP
Map dataLd GDP-MP with GTP
Sample
  • Cell: Ld GDP-MP
    • Protein or peptide: Nucleotidyl transferase family protein
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsprotozoan 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 / protein glycosylation / GTP binding / cytoplasm
Similarity search - Function
Mannose-1-phosphate guanyltransferase, N-terminal domain / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsXu W / Li H / Huang C
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971144 China
National Natural Science Foundation of China (NSFC)31770807 China
CitationJournal: 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
DepositionDec 31, 2021-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32510.png

Downloads & links

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Map

FileDownload / File: emd_32510.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLd GDP-MP with GTP
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.199
Minimum - Maximum-1.9079957 - 2.8201137
Average (Standard dev.)0.0006514443 (±0.06678297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ld GDP-MP

EntireName: Ld GDP-MP
Components
  • Cell: Ld GDP-MP
    • Protein or peptide: Nucleotidyl transferase family protein
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ld GDP-MP

SupramoleculeName: Ld GDP-MP / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Leishmania donovani (eukaryote)

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Macromolecule #1: Nucleotidyl transferase family protein

MacromoleculeName: Nucleotidyl transferase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Leishmania donovani (eukaryote)
Molecular weightTheoretical: 41.780074 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271350
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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