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- EMDB-49296: cryoEM structure of the human OGA-L Dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-49296
TitlecryoEM structure of the human OGA-L Dimer
Map datahuman OGA-L Dimer map
Sample
  • Complex: human OGA-L Catalytic Dimer
KeywordsO-GlcNAC / Histones / DNA repair / DNA Damage / Transcription / Epigenetics / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.07 Å
AuthorsNyenhuis SB / Steenackers A / Hinshaw JE / Hanover JA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Commun Chem / Year: 2025
Title: Human O-GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains.
Authors: Sarah B Nyenhuis / Agata Steenackers / Mana Mohan Mukherjee / Jenny E Hinshaw / John A Hanover /
Abstract: Although thousands of proteins are specifically O-GlcNAc modified, the molecular features recognized by the enzymes of O-GlcNAc cycling (OGT/OGA) remain poorly defined. Here we solved the structure ...Although thousands of proteins are specifically O-GlcNAc modified, the molecular features recognized by the enzymes of O-GlcNAc cycling (OGT/OGA) remain poorly defined. Here we solved the structure of the long isoform of human OGA (OGA-L) by cryo-electron microscopy (cryo-EM) providing a physiologically relevant platform to study the enzyme. The catalytic-stalk dimer structure was solved to a resolution of 3.63 Å, and the locally refined OGA A- and B-chains to 2.98 Å and 3.05 Å respectively. Intriguingly, the cryo-EM structures also exhibit lower resolution densities associated with the pHAT domains, suggesting substantial flexion of these domains relative to the catalytic-stalk dimer. OGA-L binds to a small subset of the 384 modified histone tails on a commercial histone peptide array. High affinity binding of OGA-L was detected to recombinant DNA-containing mononucleosomes bearing the H3K36 and H4K modifications. The OGA-L-H3K36 interaction was further validated by traditional ChIP experiments in MEFs. Thus, OGA-L binds to two modified histone tails of nucleosomes linked to open chromatin, whereas it does not bind to marks associated with repressive chromatin. This model is consistent with OGA-L acting as a 'reader' of histone modifications linked to development, transcriptional activation, transposon silencing, and DNA damage repair.
History
DepositionFeb 19, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49296.png

Downloads & links

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Map

FileDownload / File: emd_49296.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman OGA-L Dimer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 440 pix.
= 529.98 Å		1.2 Å/pix.
x 440 pix.
= 529.98 Å		1.2 Å/pix.
x 440 pix.
= 529.98 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0863
Minimum - Maximum-0.09321565 - 0.6952374
Average (Standard dev.)-0.00021194694 (±0.008611041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 529.98 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49296_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: human OGA-L Dimer sharpened map

Fileemd_49296_additional_1.map
Annotationhuman OGA-L Dimer sharpened map
Projections & Slices
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Half map: human OGA-L Dimer half map A

Fileemd_49296_half_map_1.map
Annotationhuman OGA-L Dimer half map A
Projections & Slices
AxesZYX

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Half map: human OGA-L Dimer half map B

Fileemd_49296_half_map_2.map
Annotationhuman OGA-L Dimer half map B
Projections & Slices
AxesZYX

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Sample components

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Entire : human OGA-L Catalytic Dimer

EntireName: human OGA-L Catalytic Dimer
Components
  • Complex: human OGA-L Catalytic Dimer

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Supramolecule #1: human OGA-L Catalytic Dimer

SupramoleculeName: human OGA-L Catalytic Dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Alphafold 2 multimer
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8527
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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