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- PDB-5bnw: The active site of O-GlcNAc transferase imposes constraints on su... -

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Basic information

Entry
Database: PDB / ID: 5bnw
TitleThe active site of O-GlcNAc transferase imposes constraints on substrate sequence
Components
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
  • laminB1 residues 179-191
KeywordsTRANSFERASE / o-glcnac transferase / glycosyl transferase
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-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / nuclear envelope organization / acetylglucosaminyltransferase activity / nuclear pore localization / regulation of Rac protein signal transduction ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / nuclear envelope organization / acetylglucosaminyltransferase activity / nuclear pore localization / regulation of Rac protein signal transduction / protein localization to nuclear envelope / regulation of necroptotic process / nuclear lamina / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / intermediate filament / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / nuclear migration / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / mitophagy / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / response to nutrient / positive regulation of TORC1 signaling / negative regulation of cell migration / positive regulation of translation / cell projection / cellular response to glucose stimulus / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / response to insulin / mitochondrial membrane / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / structural constituent of cytoskeleton / UCH proteinases / nuclear envelope / heterochromatin formation / positive regulation of cold-induced thermogenesis / HATs acetylate histones / chromatin organization / nuclear membrane / apoptotic process / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / 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 ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / 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 / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-12V / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Lamin-B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPathak, S. / Alonso, J. / Schimpl, M. / Rafie, K. / Blair, D.E. / Borodkin, V.S. / Albarbarawi, O. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT087590MA United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The active site of O-GlcNAc transferase imposes constraints on substrate sequence.
Authors: Pathak, S. / Alonso, J. / Schimpl, M. / Rafie, K. / Blair, D.E. / Borodkin, V.S. / Schuttelkopf, A.W. / Albarbarawi, O. / van Aalten, D.M.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: laminB1 residues 179-191
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9443
Polymers82,3212
Non-polymers6231
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-2 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.183, 150.176, 199.241
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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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: 80974.508 Da / Num. of mol.: 1 / Fragment: UNP residues 197-915
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide laminB1 residues 179-191


Mass: 1346.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03252*PLUS
#3: Chemical ChemComp-12V / (2S,3R,4R,5S,6R)-3-(acetylamino)-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 / URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE


Mass: 623.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O16P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.3 M DL-Malic acid pH 6.4, 0.1 M Bis-Tris propane pH 6.4 supplemented with crystal seeds grown out of the same condition.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2015 / Details: Pilatus 2M Detector
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 263631 / Num. obs: 40463 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDS0.5data reduction
SCALA3.3.21data scaling
Coot0.7.2model building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.831 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23517 2022 5 %RANDOM
Rwork0.18736 ---
obs0.18981 38435 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2--2.89 Å20 Å2
3----1.4 Å2
Refinement stepCycle: 1 / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 39 78 5650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195705
X-RAY DIFFRACTIONr_bond_other_d0.0020.025461
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9637739
X-RAY DIFFRACTIONr_angle_other_deg0.823.00212574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51224.521261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77915981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4211531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216426
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021299
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0274.3642804
X-RAY DIFFRACTIONr_mcbond_other3.0274.3632803
X-RAY DIFFRACTIONr_mcangle_it4.5846.5353498
X-RAY DIFFRACTIONr_mcangle_other4.5846.5373499
X-RAY DIFFRACTIONr_scbond_it3.4244.7262899
X-RAY DIFFRACTIONr_scbond_other3.4234.7262899
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5156.924242
X-RAY DIFFRACTIONr_long_range_B_refined7.57334.3256521
X-RAY DIFFRACTIONr_long_range_B_other7.57734.3336504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 158 -
Rwork0.31 2788 -
obs--99.97 %

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