[English] 日本語
Yorodumi
- EMDB-32511: Cryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32511
TitleCryo-EM Structure of Leishmanial GDP-mannose pyrophosphorylase in complex with GDP-Mannose
Map dataLd GDP-MP with GDP-Mannose
Sample
  • Cell: Ld GDP-MP
    • Protein or peptide: Nucleotidyl transferase family protein
  • Ligand: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
  • 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 / GTP binding
Similarity search - Function
Mannose-1-phosphate guanyltransferase, N-terminal domain / : / GMPPB C-terminal domain / : / Nucleotidyl transferase domain / Nucleotidyl transferase / 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: 3.5 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) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32511.png

Downloads & links

-
Map

FileDownload / File: emd_32511.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLd GDP-MP with GDP-Mannose
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.142
Minimum - Maximum-1.2943354 - 2.0527003
Average (Standard dev.)0.0009144063 (±0.0509537)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : Ld GDP-MP

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

-
Supramolecule #1: Ld GDP-MP

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

-
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

-
Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / type: ligand / ID: 2 / Number of copies: 6 / Formula: GDD
Molecular weightTheoretical: 605.341 Da
Chemical component information

ChemComp-GDD:
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE

-
Macromolecule #3: MAGNESIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123461
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more