[English] 日本語
Yorodumi
- PDB-6e37: O-GlcNAc Transferase in complex with covalent inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+37
TitleO-GlcNAc Transferase in complex with covalent inhibitor
Components
  • O-GlcNAc transferase subunit p110
  • TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
KeywordsTRANSFERASE/Inhibitor / O-GlcNAc Transferase / inhibitor / TRANSFERASE-Inhibitor complex
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / protein O-linked glycosylation ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / protein O-linked glycosylation / negative regulation of stem cell population maintenance / regulation of gluconeogenesis / Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK / positive regulation of aggrephagy / regulation of chromosome separation / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / regulation of glycolytic process / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / RIPK1-mediated regulated necrosis / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / Receptor Mediated Mitophagy / Sin3-type complex / Formation of WDR5-containing histone-modifying complexes / regulation of synapse assembly / hemopoiesis / positive regulation of stem cell population maintenance / Synthesis of PC / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of apoptotic signaling pathway / positive regulation of proteolysis / negative regulation of signal transduction by p53 class mediator / phosphatidylinositol-3,4,5-trisphosphate binding / Maturation of hRSV A proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / histone acetyltransferase complex / negative regulation of double-strand break repair via homologous recombination / mitophagy / positive regulation of Wnt signaling pathway / cell projection / response to nutrient / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / Signal transduction by L1 / positive regulation of translation / protein processing / cellular response to glucose stimulus / circadian regulation of gene expression / Wnt signaling pathway / response to insulin / Hsp90 protein binding / chromatin DNA binding / peptidyl-serine phosphorylation / PML body / Regulation of necroptotic cell death / mitochondrial membrane / SPOP-mediated proteasomal degradation of PD-L1(CD274) / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / double-strand break repair / KEAP1-NFE2L2 pathway / rhythmic process / UCH proteinases / positive regulation of cell growth / positive regulation of cold-induced thermogenesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / HATs acetylate histones / protein folding / heterochromatin formation / chromatin organization / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / non-specific serine/threonine protein kinase / protein stabilization / negative regulation of translation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HQV / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.531 Å
AuthorsLi, H. / Jiang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121718 United States
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Targeted covalent inhibition of O-GlcNAc transferase in cells.
Authors: Worth, M. / Hu, C.W. / Li, H. / Fan, D. / Estevez, A. / Zhu, D. / Wang, A. / Jiang, J.
History
DepositionJul 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: O-GlcNAc transferase subunit p110
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0233
Polymers82,3732
Non-polymers6491
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area27500 Å2
MethodPISA
2
A: O-GlcNAc transferase subunit p110
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
hetero molecules

A: O-GlcNAc transferase subunit p110
B: TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0456
Polymers164,7464
Non-polymers1,2992
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544x,-y-1/2,-z-1/21
Buried area6910 Å2
ΔGint-27 kcal/mol
Surface area50570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.656, 150.984, 198.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1230-

HOH

-
Components

#1: Protein O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGUDP-N-acetylglucosamine--peptide N- ...O-linked N-acetylglucosamine transferase 110 kDa subunit / OGUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunitT


Mass: 80974.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide TYR-PRO-GLY-GLY-SER-THR-PRO-VAL-SER-SER-ALA-ASN


Mass: 1398.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68400*PLUS
#3: Chemical ChemComp-HQV / (2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 649.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N3O16P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.45 M potassium phosphate dibasic 10 mM EDTA 1% xylitol

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 34188 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.992 / Net I/σ(I): 16
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1313 / CC1/2: 0.932 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14rc1_3161: ???)refinement
HKL-20002.3.8data scaling
HKL-20002.3.8data scaling
Cootmodel building
RefinementResolution: 2.531→41.525 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 1705 4.99 %
Rwork0.1671 --
obs0.1693 34179 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.531→41.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 41 191 5780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085741
X-RAY DIFFRACTIONf_angle_d0.9687801
X-RAY DIFFRACTIONf_dihedral_angle_d14.2823471
X-RAY DIFFRACTIONf_chiral_restr0.053864
X-RAY DIFFRACTIONf_plane_restr0.0061013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5312-2.60570.25021200.21662458X-RAY DIFFRACTION90
2.6057-2.68980.27251600.20042720X-RAY DIFFRACTION100
2.6898-2.78590.27791400.20062641X-RAY DIFFRACTION99
2.7859-2.89740.2411520.19482705X-RAY DIFFRACTION100
2.8974-3.02920.26561340.18452731X-RAY DIFFRACTION100
3.0292-3.18890.24951540.18782722X-RAY DIFFRACTION100
3.1889-3.38860.24581240.17252734X-RAY DIFFRACTION100
3.3886-3.65010.21761490.16042731X-RAY DIFFRACTION100
3.6501-4.01710.19651490.13932720X-RAY DIFFRACTION100
4.0171-4.59780.1541450.12682734X-RAY DIFFRACTION100
4.5978-5.79020.16551370.14792755X-RAY DIFFRACTION99
5.7902-41.53060.20931410.19212823X-RAY DIFFRACTION98

+
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