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- PDB-7wht: Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in... -

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Basic information

Entry
Database: PDB / ID: 7wht
TitleCryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in complex with GDP-Mannose
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 / : / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / mannose-1-phosphate guanylyltransferase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 1.0Oct 12, 2022Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)254,45818
Polymers250,6806
Non-polymers3,77812
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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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
#2: Chemical
ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H25N5O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: #1 / 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 K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123461 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00317418
ELECTRON MICROSCOPYf_angle_d0.51823610
ELECTRON MICROSCOPYf_dihedral_angle_d4.3512316
ELECTRON MICROSCOPYf_chiral_restr0.052658
ELECTRON MICROSCOPYf_plane_restr0.0063006

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