[English] 日本語
Yorodumi
- EMDB-63590: Imidazole glycerol phosphate dehydratase from Mycobacterium tuber... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63590
TitleImidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure
Map dataCombined, sharpened map
Sample
  • Complex: Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizole added but not modelled
    • Protein or peptide: Imidazoleglycerol-phosphate dehydratase
  • Ligand: MANGANESE (II) ION
  • Ligand: water
Keywordshistidine pathway / dehydratase / Mycobacterium tuberculosis / LYASE
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsRaina R / Kar D / Singla M / Tiwari S / Kumari S / Aneja S / Kumar V / Banerjee S / Goyal S / Pal RK ...Raina R / Kar D / Singla M / Tiwari S / Kumari S / Aneja S / Kumar V / Banerjee S / Goyal S / Pal RK / Vinothkumar KR / Biswal BK
Funding support India, 4 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/TIF/09/02/2021-22 India
Department of Biotechnology (DBT, India)BT/PR29075/BRB/10/1699/2018 India
Department of Biotechnology (DBT, India)BT/PR40325/BTIS/137/1/2020 India
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/2014 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2025
Title: Cryo-EM structures of Mycobacterium tuberculosis imidazole glycerol phosphate dehydratase in the apo state and in the presence of small molecules.
Authors: Rahul Raina / Deepsikha Kar / Mohini Singla / Satish Tiwari / Swati Kumari / Sonanjali Aneja / Varun Kumar / Soumya Banerjee / Shivika Goyal / Ravi Kant Pal / Kutti R Vinothkumar / Bichitra Biswal /
Abstract: Unlike humans, Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, has a de novo histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), ...Unlike humans, Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis, has a de novo histidine-biosynthesis pathway. The enzyme imidazole glycerol phosphate dehydratase (IGPD), which catalyses the conversion of imidazole glycerol phosphate to imidazole acetol phosphate, has been studied extensively from various organisms and has become a major target for the development of antibacterial, antiweed and antifungal small molecules. In our previous studies, we have shown that in crystals IGPD forms a 24-mer oligomeric state in which the monomers are arranged in 432 symmetry. In order to gain insights into the oligomeric state of Mtb IGPD in solution, we determined cryogenic sample electron microscopy (cryo-EM) structures of apo IGPD at 2.2 and 3.1 Å resolution. In addition, we also determined the cryo-EM structure of IGPD in the presence of 3-amino-1,2,4-triazole (ATZ) to 2.8 Å resolution. The results of this work, which corroborate those from the crystallographic studies, indicate that IGPD forms a homo-oligomeric structure in solution comprising of 24 subunits. ATZ binds in the active-site pocket of the enzyme, which is located at the interface of three monomers and tethers 24 ATZ molecules. The results of this study suggest that cryo-EM, in addition to being a rapidly evolving and complementary imaging technology for elucidating 3D structures of biological macromolecules, can be useful in pinpointing the mode of binding small molecules of low mass (here ∼85 Da) and mapping protein-ligand interactions, which could assist in the design of accurate (high-potency) inhibitors.
History
DepositionFeb 28, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63590.png

Downloads & links

-
Map

FileDownload / File: emd_63590.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined, sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.13018265 - 0.25222492
Average (Standard dev.)0.00043537628 (±0.013203024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: one of the half maps

Fileemd_63590_half_map_1.map
Annotationone of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: one of the half maps

Fileemd_63590_half_map_2.map
Annotationone of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizol...

EntireName: Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizole added but not modelled
Components
  • Complex: Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizole added but not modelled
    • Protein or peptide: Imidazoleglycerol-phosphate dehydratase
  • Ligand: MANGANESE (II) ION
  • Ligand: water

-
Supramolecule #1: Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizol...

SupramoleculeName: Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizole added but not modelled
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: An oligomer of 24 subunits
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 550 KDa

-
Macromolecule #1: Imidazoleglycerol-phosphate dehydratase

MacromoleculeName: Imidazoleglycerol-phosphate dehydratase / type: protein_or_peptide / ID: 1
Details: The enzyme was expressed with a Histag at the N-terminus but not observed in the experiment. The C-terminal residues are also not observed in the experiment. The original uniprot ID doesn't ...Details: The enzyme was expressed with a Histag at the N-terminus but not observed in the experiment. The C-terminal residues are also not observed in the experiment. The original uniprot ID doesn't exist (I6XBW5) but uniparc ID is UPI000012C861.
Number of copies: 24 / Enantiomer: LEVO / EC number: imidazoleglycerol-phosphate dehydratase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 23.633516 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis (bacteria)
SequenceString: MHHHHHHTTT QTAKASRRAR IERRTRESDI VIELDLDGTG QVAVDTGVPF YDHMLTALGS HASFDLTVRA TGDVEIEAHH TIEDTAIAL GTALGQALGD KRGIRRFGDA FIPMDETLAH AAVDLSGRPY CVHTGEPDHL QHTTIAGSSV PYHTVINRHV F ESLAANAR ...String:
MHHHHHHTTT QTAKASRRAR IERRTRESDI VIELDLDGTG QVAVDTGVPF YDHMLTALGS HASFDLTVRA TGDVEIEAHH TIEDTAIAL GTALGQALGD KRGIRRFGDA FIPMDETLAH AAVDLSGRPY CVHTGEPDHL QHTTIAGSSV PYHTVINRHV F ESLAANAR IALHVRVLYG RDPHHITEAQ YKAVARALRQ AVEPDPRVSG VPSTKGAL

UniProtKB: Imidazoleglycerol-phosphate dehydratase

-
Macromolecule #2: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 48 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1032 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 8.5
Component:
ConcentrationNameFormula
20.0 mMTris
200.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsBefore freezing, 0.5% chapso and 100 uM BrATZ (5-bromo-1-propyl-1H-1,2,4-traizole) was added

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 40.0 sec. / Average electron dose: 26.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 166666 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 35.0 µm / Nominal defocus min: 12.0 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 150382
CTF correctionSoftware: (Name: CTFFIND (ver. 4.1), RELION (ver. 4.0)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-intio using Relion
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 96264
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4lpf


Chain - Chain ID: A / Chain - Residue range: 10-199 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 103.3
Output model

PDB-9m2r:
Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure

+
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