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- PDB-6tka: Crystal structure of human O-GlcNAc transferase bound to substrat... -

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Basic information

Entry
Database: PDB / ID: 6tka
TitleCrystal structure of human O-GlcNAc transferase bound to substrate 7 and a peptide from HCF-1 pro-repeat 2 (11-26)
Components
  • HCF-1 pro-repeat 2 (11-26)
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / Transferase Complex O-GlcNAc OGT
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 / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / 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
Chem-NG8 / Chem-NJ5 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsMeek, R.W. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal SocietyRPEA180016 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: A Direct Fluorescent Activity Assay for Glycosyltransferases Enables Convenient High-Throughput Screening: Application to O-GlcNAc Transferase.
Authors: Alteen, M.G. / Gros, C. / Meek, R.W. / Cardoso, D.A. / Busmann, J.A. / Sangouard, G. / Deen, M.C. / Tan, H.Y. / Shen, D.L. / Russell, C.C. / Davies, G.J. / Robinson, P.J. / McCluskey, A. / Vocadlo, D.J.
History
DepositionNov 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
BBB: HCF-1 pro-repeat 2 (11-26)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0664
Polymers82,9982
Non-polymers1,0692
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
BBB: HCF-1 pro-repeat 2 (11-26)
hetero molecules

AAA: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
BBB: HCF-1 pro-repeat 2 (11-26)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,1338
Polymers165,9954
Non-polymers2,1374
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)100.859, 100.859, 132.629
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11AAA-1277-

HOH

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Components

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGT


Mass: 81388.969 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 BL21(DE3) (bacteria) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide HCF-1 pro-repeat 2 (11-26)


Mass: 1608.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NJ5 / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[6-(butanoylamino)hexanoylamino]-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 748.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H42N4O18P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NG8 / 3-[2,2-bis(fluoranyl)-10,12-dimethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-4,6,9,11-tetraen-4-yl]-~{N}-ethyl-propanamide


Mass: 320.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21BF2N3O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.45 M Potassium Sodium Tartrate 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.91→87.32 Å / Num. obs: 61015 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.03 / Rrim(I) all: 0.104 / Χ2: 0.95 / Net I/σ(I): 15.6
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4473 / CC1/2: 0.405 / Rpim(I) all: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n39

4n39


Resolution: 1.91→72.95 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 3089 5.067 %Random Selection
Rwork0.1845 ---
all0.187 ---
obs-60965 99.962 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.162 Å20.081 Å20 Å2
2--0.162 Å2-0 Å2
3----0.527 Å2
Refinement stepCycle: LAST / Resolution: 1.91→72.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 72 208 5845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135819
X-RAY DIFFRACTIONr_bond_other_d0.0350.0175341
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6467916
X-RAY DIFFRACTIONr_angle_other_deg2.31.57112451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2985718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08115987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9151530
X-RAY DIFFRACTIONr_chiral_restr0.0730.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026480
X-RAY DIFFRACTIONr_gen_planes_other0.010.021144
X-RAY DIFFRACTIONr_nbd_refined0.2050.21220
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24901
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22808
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.22348
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.221
X-RAY DIFFRACTIONr_nbd_other0.2070.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.214
X-RAY DIFFRACTIONr_mcbond_it2.9933.9312846
X-RAY DIFFRACTIONr_mcbond_other2.9893.932845
X-RAY DIFFRACTIONr_mcangle_it3.8435.883556
X-RAY DIFFRACTIONr_mcangle_other3.8435.8813557
X-RAY DIFFRACTIONr_scbond_it3.5984.3122973
X-RAY DIFFRACTIONr_scbond_other3.5924.3132973
X-RAY DIFFRACTIONr_scangle_it5.2346.3154353
X-RAY DIFFRACTIONr_scangle_other5.2366.3164354
X-RAY DIFFRACTIONr_lrange_it6.35546.6056493
X-RAY DIFFRACTIONr_lrange_other6.35546.6126494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.3522190.3194239X-RAY DIFFRACTION99.7539
1.96-2.0140.3132520.2924100X-RAY DIFFRACTION99.977
2.014-2.0720.2742000.2623993X-RAY DIFFRACTION100
2.072-2.1360.3061790.2423953X-RAY DIFFRACTION99.9758
2.136-2.2060.2622090.2253764X-RAY DIFFRACTION99.9497
2.206-2.2830.2561900.2053675X-RAY DIFFRACTION100
2.283-2.3690.2871760.2083541X-RAY DIFFRACTION100
2.369-2.4660.2671800.2013421X-RAY DIFFRACTION99.9722
2.466-2.5760.281770.2013270X-RAY DIFFRACTION100
2.576-2.7010.2892050.2033090X-RAY DIFFRACTION100
2.701-2.8470.2571380.1913010X-RAY DIFFRACTION100
2.847-3.020.2581680.1922812X-RAY DIFFRACTION100
3.02-3.2280.2151410.1952680X-RAY DIFFRACTION100
3.228-3.4870.2611210.1792513X-RAY DIFFRACTION100
3.487-3.820.1911110.1632297X-RAY DIFFRACTION100
3.82-4.270.1761360.1432069X-RAY DIFFRACTION100
4.27-4.930.201980.1391861X-RAY DIFFRACTION100
4.93-6.0350.206830.1581596X-RAY DIFFRACTION100
6.035-8.5270.189660.1561248X-RAY DIFFRACTION100
8.527-72.950.221400.185744X-RAY DIFFRACTION99.8726

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