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- PDB-7whr: Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase -

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Basic information

Entry
Database: PDB / ID: 7whr
TitleCryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase
ComponentsNucleotidyl transferase family protein
KeywordsSUGAR BINDING PROTEIN / protozoan enzyme / Leishmania donovani
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
Mannose-1-phosphate guanyltransferase, N-terminal domain / : / GMPPB C-terminal domain / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A ...Mannose-1-phosphate guanyltransferase, N-terminal domain / : / GMPPB C-terminal domain / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXu, W. / Li, H. / Huang, C.
Funding support China, 2items
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.0Sep 21, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 21, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 21, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 21, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 21, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleotidyl transferase family protein
A: Nucleotidyl transferase family protein
C: Nucleotidyl transferase family protein
D: Nucleotidyl transferase family protein
E: Nucleotidyl transferase family protein
F: Nucleotidyl transferase family protein


Theoretical massNumber of molelcules
Total (without water)250,6806
Polymers250,6806
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7750 Å2
ΔGint-63 kcal/mol
Surface area95300 Å2

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Components

#1: Protein
Nucleotidyl transferase family protein


Mass: 41780.074 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: CGC21_17635 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A504XPK0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ld GDP-MP / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Leishmania donovani (eukaryote)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56825 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317274
ELECTRON MICROSCOPYf_angle_d0.57723376
ELECTRON MICROSCOPYf_dihedral_angle_d4.6022316
ELECTRON MICROSCOPYf_chiral_restr0.052610
ELECTRON MICROSCOPYf_plane_restr0.0053024

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