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- EMDB-49294: cryoEM structure of the A-chain of the human OGA-L Catalytic Dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-49294
TitlecryoEM structure of the A-chain of the human OGA-L Catalytic Dimer
Map dataOGA-L Catalytic A-chain map
Sample
  • Complex: A-chain of the human OGA-L Catalytic Dimer
    • Protein or peptide: Protein O-GlcNAcase
KeywordsO-GlcNAC / Histones / DNA repair / DNA Damage / Transcription / Epigenetics / HYDROLASE
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Acyl-CoA N-acyltransferase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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_49294.png

Downloads & links

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Map

FileDownload / File: emd_49294.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOGA-L Catalytic A-chain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 280 pix.
= 339.192 Å		1.21 Å/pix.
x 280 pix.
= 339.192 Å		1.21 Å/pix.
x 280 pix.
= 339.192 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.177
Minimum - Maximum-1.5379183 - 2.3186533
Average (Standard dev.)0.000026565134 (±0.021693293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 339.19202 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49294_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: OGA-L Catalytic A-chain sharpened map

Fileemd_49294_additional_1.map
AnnotationOGA-L Catalytic A-chain sharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: OGA-L Catalytic A-chain half map A

Fileemd_49294_half_map_1.map
AnnotationOGA-L Catalytic A-chain half map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: OGA-L Catalytic A-chain half map B

Fileemd_49294_half_map_2.map
AnnotationOGA-L Catalytic A-chain half map B
Projections & Slices
AxesZYX

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Sample components

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Entire : A-chain of the human OGA-L Catalytic Dimer

EntireName: A-chain of the human OGA-L Catalytic Dimer
Components
  • Complex: A-chain of the human OGA-L Catalytic Dimer
    • Protein or peptide: Protein O-GlcNAcase

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Supramolecule #1: A-chain of the human OGA-L Catalytic Dimer

SupramoleculeName: A-chain of the human OGA-L Catalytic Dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein O-GlcNAcase

MacromoleculeName: Protein O-GlcNAcase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein O-GlcNAcase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.020906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVQKESQATL EERESELSSN PAASAGASLE PPAAPAPGED NPAGAGGAAV AGAAGGARRF LCGVVEGFYG RPWVMEQRKE LFRRLQKWE LNTYLYAPKD DYKHRMFWRE MYSVEEAEQL MTLISAAREY EIEFIYAISP GLDITFSNPK EVSTLKRKLD Q VSQFGCRS ...String:
MVQKESQATL EERESELSSN PAASAGASLE PPAAPAPGED NPAGAGGAAV AGAAGGARRF LCGVVEGFYG RPWVMEQRKE LFRRLQKWE LNTYLYAPKD DYKHRMFWRE MYSVEEAEQL MTLISAAREY EIEFIYAISP GLDITFSNPK EVSTLKRKLD Q VSQFGCRS FALLFDDIDH NMCAADKEVF SSFAHAQVSI TNEIYQYLGE PETFLFCPTE YCGTFCYPNV SQSPYLRTVG EK LLPGIEV LWTGPKVVSK EIPVESIEEV SKIIKRAPVI WDNIHANDYD QKRLFLGPYK GRSTELIPRL KGVLTNPNCE FEA NYVAIH TLATWYKSNM NGVRKDVVMT DSEDSTVSIQ IKLENEGSDE DIETDVLYSP QMALKLALTE WLQEFGVPHQ YSSR QVAHS GAKASVVDGT PLVAAPSLNA TTVVTTVYQE PIMSQGAALS GEPTTLTKEE EKKQPDEEPM DMVVEKQEET DHKND NQIL SEIVEAKMAE ELKPMDTDKE SIAESKSPEM SMQEDCISDI APMQTDEQTN KEQFVPGPNE KPLYTAEPVT LEDLQL LAD LFYLPYEHGP KGAQMLREFQ WLRANSSVVS VNCKGKDSEK IEEWRSRAAK FEEMCGLVMG MFTRLSNCAN RTILYDM YS YVWDIKSIMS MVKSFVQWLG CRSHSSAQFL IGDQEPWAFR GGLAGEFQRL LPIDGANDLF FQPPPLTPTS KVYTIRPY F PKDEASVYKI CREMYDDGVG LPFQSQPDLI GDKLVGGLLS LSLDYCFVLE DEDGICGYAL GTVDVTPFIK KCKISWIPF MQEKYTKPNG DKELSEAEKI MLSFHEEQEV LPETFLANFP SLIKMDIHKK VTDPSVAKSM MACLLSSLKA NGSRGAFCEV RPDDKRILE FYSKLGCFEI AKMEGFPKDV VILGRSL

UniProtKB: Protein O-GlcNAcase

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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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65831
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
Output model

PDB-9ne4:
cryoEM structure of the A-chain of the human OGA-L Catalytic Dimer

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