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- EMDB-19693: Hexameric worm glutamate dehydrogenase (C136S) -

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Basic information

Entry
Database: EMDB / ID: EMD-19693
TitleHexameric worm glutamate dehydrogenase (C136S)
Map data
Sample
  • Complex: Hexameric complex of Glutamatedehydrogenase (C136S)
    • Protein or peptide: Hexameric worm glutamate dehydrogenase (C136S)
Keywordsdehydrogenase / glutamate / immunoregulatory function / OXIDOREDUCTASE
Biological speciesHeligmosomoides bakeri (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsBohnacker S / Bohn S / Sattler M / Esser-von Bieren J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Immunol / Year: 2024
Title: A helminth enzyme subverts macrophage-mediated immunity by epigenetic targeting of prostaglandin synthesis.
Authors: Sina Bohnacker / Fiona D R Henkel / Franziska Hartung / Arie Geerlof / Sandra Riemer / Ulrich F Prodjinotho / Eya Ben Salah / André Santos Dias Mourão / Stefan Bohn / Tarvi Teder / ...Authors: Sina Bohnacker / Fiona D R Henkel / Franziska Hartung / Arie Geerlof / Sandra Riemer / Ulrich F Prodjinotho / Eya Ben Salah / André Santos Dias Mourão / Stefan Bohn / Tarvi Teder / Dominique Thomas / Robert Gurke / Christiane Boeckel / Minhaz Ud-Dean / Ann-Christine König / Alessandro Quaranta / Francesca Alessandrini / Antonie Lechner / Benedikt Spitzlberger / Agnieszka M Kabat / Edward Pearce / Jesper Z Haeggström / Stefanie M Hauck / Craig E Wheelock / Per-Johan Jakobsson / Michael Sattler / David Voehringer / Matthias J Feige / Clarissa Prazeres da Costa / Julia Esser-von Bieren /
Abstract: The molecular mechanisms by which worm parasites evade host immunity are incompletely understood. In a mouse model of intestinal helminth infection using (), we show that helminthic glutamate ...The molecular mechanisms by which worm parasites evade host immunity are incompletely understood. In a mouse model of intestinal helminth infection using (), we show that helminthic glutamate dehydrogenase (heGDH) drives parasite chronicity by suppressing macrophage-mediated host defense. Combining RNA-seq, ChIP-seq, and targeted lipidomics, we identify prostaglandin E (PGE) as a major immune regulatory mechanism of heGDH. The induction of PGE and other immunoregulatory factors, including IL-12 family cytokines and indoleamine 2,3-dioxygenase 1, by heGDH required p300-mediated histone acetylation, whereas the enzyme's catalytic activity suppressed the synthesis of type 2-promoting leukotrienes by macrophages via 2-hydroxyglutarate. By contrast, the induction of immunoregulatory factors involved the heGDH N terminus by potentially mediating interactions with cellular targets (CD64 and GPNMB) identified by proteomics. Type 2 cytokines counteracted suppressive effects of heGDH on host defense, indicating that type 2 immunity can limit helminth-driven immune evasion. Thus, helminths harness a ubiquitous metabolic enzyme to epigenetically target type 2 macrophage activation and establish chronicity.
History
DepositionFeb 20, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19693.png

Downloads & links

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Map

FileDownload / File: emd_19693.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 448 pix.
= 255.36 Å		0.57 Å/pix.
x 448 pix.
= 255.36 Å		0.57 Å/pix.
x 448 pix.
= 255.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0377
Minimum - Maximum-0.08634763 - 0.22567086
Average (Standard dev.)0.0010839477 (±0.0088948915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 255.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19693_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19693_half_map_2.map
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Sample components

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Entire : Hexameric complex of Glutamatedehydrogenase (C136S)

EntireName: Hexameric complex of Glutamatedehydrogenase (C136S)
Components
  • Complex: Hexameric complex of Glutamatedehydrogenase (C136S)
    • Protein or peptide: Hexameric worm glutamate dehydrogenase (C136S)

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Supramolecule #1: Hexameric complex of Glutamatedehydrogenase (C136S)

SupramoleculeName: Hexameric complex of Glutamatedehydrogenase (C136S) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Heligmosomoides bakeri (invertebrata)
Molecular weightTheoretical: 363 KDa

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Macromolecule #1: Hexameric worm glutamate dehydrogenase (C136S)

MacromoleculeName: Hexameric worm glutamate dehydrogenase (C136S) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MLSTLARTSG RLIFRRALSS AQMDAHAQVI DDLKPMEEQS NPSFFKMVDY YFDKGATVIE PKLVEEMKSN SMSVMDKKNL VSGILKAIKP VNKVLYITFP IRRDNGEFEV VEAWRAQHSE HRTPTKGGIR YSLDVSEDEV KALSALMTYK CAAVDVPFGG AKGGVKIDPK ...String:
MLSTLARTSG RLIFRRALSS AQMDAHAQVI DDLKPMEEQS NPSFFKMVDY YFDKGATVIE PKLVEEMKSN SMSVMDKKNL VSGILKAIKP VNKVLYITFP IRRDNGEFEV VEAWRAQHSE HRTPTKGGIR YSLDVSEDEV KALSALMTYK CAAVDVPFGG AKGGVKIDPK MYTDYEIEKI TRRIAIEFAK KGFLGPGVDV PAPDMGTGER EMGWIADTYA QTIGHLDRDA SACITGKPIV AGGIHGRVSA TGRGVWKGLE VFAKEPEYME KIGLTPGLPG KTVIIQGFGN VGLHTMRYLH RAGSKVVGIQ EWDCAIHNPA GIHPKELEDW RDQTGSIKNF PGAKNFEPFG DLIYEACDIL VPAACEKAIH KENAGRIQAK IIAEAANGPT TPAADKILLE RGNCLIIPDM YVNSGGVTVS YFEWLKNLNH VSYGRLSFKY EEDANLMLLQ SVQDSLEKAI GKEAPVRPNA QFAAKIAGAS EKDIVHSGLE YTMARSGEAI IRTARKYNLG LDMRTAAYAN SIEKVYNTYR TAGFTFT

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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

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1803297
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 232867
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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