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- EMDB-33768: Human O-GlcNAc transferase Dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-33768
TitleHuman O-GlcNAc transferase Dimer
Map dataHuman OGT Dimer
Sample
  • Complex: Human O-GlcNAc transferase (OGT)
    • Protein or peptide: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsHuman O-GlcNAc transferase Dimer / TRANSFERASE
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of proteolysis / mitophagy / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / negative regulation of cell migration / response to nutrient / cell projection / positive regulation of translation / mitochondrial membrane / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / glutamatergic synapse / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsGao H / Lu P / Liu Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130053 China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of human O-GlcNAcylation enzyme pair OGT-OGA complex.
Authors: Ping Lu / Yusong Liu / Maozhou He / Ting Cao / Mengquan Yang / Shutao Qi / Hongtao Yu / Haishan Gao /
Abstract: O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O- ...O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O-GlcNAcylation regulates diverse cellular processes by modulating the stability, structure, and function of target proteins. Dysregulation of O-GlcNAcylation has been implicated in the pathogenesis of cancer, diabetes, and neurodegeneration. A single pair of enzymes, the O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), catalyzes the addition and removal of O-GlcNAc on over 3,000 proteins in the human proteome. However, how OGT selects its native substrates and maintains the homeostatic control of O-GlcNAcylation of so many substrates against OGA is not fully understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of human OGT and the OGT-OGA complex. Our studies reveal that OGT forms a functionally important scissor-shaped dimer. Within the OGT-OGA complex structure, a long flexible OGA segment occupies the extended substrate-binding groove of OGT and positions a serine for O-GlcNAcylation, thus preventing OGT from modifying other substrates. Conversely, OGT disrupts the functional dimerization of OGA and occludes its active site, resulting in the blocking of access by other substrates. This mutual inhibition between OGT and OGA may limit the futile O-GlcNAcylation cycles and help to maintain O-GlcNAc homeostasis.
History
DepositionJul 5, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33768.png

Downloads & links

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Map

FileDownload / File: emd_33768.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman OGT Dimer
Voxel sizeX=Y=Z: 0.861 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.137122 - 3.5585766
Average (Standard dev.)-0.00008947747 (±0.042943712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 344.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map

Fileemd_33768_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_33768_half_map_2.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human O-GlcNAc transferase (OGT)

EntireName: Human O-GlcNAc transferase (OGT)
Components
  • Complex: Human O-GlcNAc transferase (OGT)
    • Protein or peptide: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

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Supramolecule #1: Human O-GlcNAc transferase (OGT)

SupramoleculeName: Human O-GlcNAc transferase (OGT) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase ...

MacromoleculeName: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein O-GlcNAc transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 117.937367 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MASSVGNVAD STEPTKRMLS FQGPMELAHR EYQAGDFEAA ERHCMQLWRQ EPDNTGVLLL LSSIHFECRR LDRSAHFSTL AIKQNPLLA EAYSNLGNVY KERGQLQEAI EHYRHALRLK PDFIDGYINL AAALVAAGDM EGAVQAYVSA LQYNPDLYCV R SDLGNLLK ...String:
MASSVGNVAD STEPTKRMLS FQGPMELAHR EYQAGDFEAA ERHCMQLWRQ EPDNTGVLLL LSSIHFECRR LDRSAHFSTL AIKQNPLLA EAYSNLGNVY KERGQLQEAI EHYRHALRLK PDFIDGYINL AAALVAAGDM EGAVQAYVSA LQYNPDLYCV R SDLGNLLK ALGRLEEAKA CYLKAIETQP NFAVAWSNLG CVFNAQGEIW LAIHHFEKAV TLDPNFLDAY INLGNVLKEA RI FDRAVAA YLRALSLSPN HAVVHGNLAC VYYEQGLIDL AIDTYRRAIE LQPHFPDAYC NLANALKEKG SVAEAEDCYN TAL RLCPTH ADSLNNLANI KREQGNIEEA VRLYRKALEV FPEFAAAHSN LASVLQQQGK LQEALMHYKE AIRISPTFAD AYSN MGNTL KEMQDVQGAL QCYTRAIQIN PAFADAHSNL ASIHKDSGNI PEAIASYRTA LKLKPDFPDA YCNLAHCLQI VCDWT DYDE RMKKLVSIVA DQLEKNRLPS VHPHHSMLYP LSHGFRKAIA ERHGNLCLDK INVLHKPPYE HPKDLKLSDG RLRVGY VSS DFGNHPTSHL MQSIPGMHNP DKFEVFCYAL SPDDGTNFRV KVMAEANHFI DLSQIPCNGK AADRIHQDGI HILVNMN GY TKGARNELFA LRPAPIQAMW LGYPGTSGAL FMDYIITDQE TSPAEVAEQY SEKLAYMPHT FFIGDHANMF PHLKKKAV I DFKSNGHIYD NRIVLNGIDL KAFLDSLPDV KIVKMKCPDG GDNADSSNTA LNMPVIPMNT IAEAVIEMIN RGQIQITIN GFSISNGLAT TQINNKAATG EEVPRTIIVT TRSQYGLPED AIVYCNFNQL YKIDPSTLQM WANILKRVPN SVLWLLRFPA VGEPNIQQY AQNMGLPQNR IIFSPVAPKE EHVRRGQLAD VCLDTPLCNG HTTGMDVLWA GTPMVTMPGE TLASRVAASQ L TCLGCLEL IAKNRQEYED IAVKLGTDLE YLKKVRGKVW KQRISSPLFN TKQYTMELER LYLQMWEHYA AGNKPDHMIK PV EVTESAH HHHHH

UniProtKB: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit

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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

Concentration5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5539 / Average exposure time: 0.0725 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6266880
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3pe3


Details: 1W3B, 3PE3
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 124155

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Atomic model buiding 1

Initial modelPDB ID:

3pe3


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 137
Output model

PDB-7yea:
Human O-GlcNAc transferase Dimer

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