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- PDB-8fuf: Crystal structure of human O-GlcNAc transferase (OGT) in complex ... -

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Basic information

Entry
Database: PDB / ID: 8fuf
TitleCrystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (ZNF831) and UDP-GlcNAc
Components
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
  • Zinc finger protein 831
KeywordsTRANSFERASE / O-GlcNAc transferase / exosite / protein-protein interaction / 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-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance ...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 / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / 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 / UCH proteinases / positive regulation of cold-induced thermogenesis / HATs acetylate histones / chromatin organization / 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 / metal ion binding / nucleus / plasma membrane / cytosol
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 / Tetratricopeptide repeat ...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 / Tetratricopeptide repeat / Glycogen Phosphorylase B; / Zinc finger, C2H2 type / zinc finger / TPR repeat region circular profile. / TPR repeat profile. / Zinc finger C2H2 type domain profile. / Tetratricopeptide repeats / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Tetratricopeptide repeat / Zinc finger C2H2-type / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Zinc finger protein 831
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å
AuthorsXie, J. / 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: Nat.Chem.Biol. / Year: 2023
Title: Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase.
Authors: Blankenship, C.M. / Xie, J. / Benz, C. / Wang, A. / Ivarsson, Y. / Jiang, J.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
B: Zinc finger protein 831
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Zinc finger protein 831
E: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: Zinc finger protein 831
G: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: Zinc finger protein 831
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,52312
Polymers330,0938
Non-polymers2,4294
Water00
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Zinc finger protein 831
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1313
Polymers82,5232
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-17 kcal/mol
Surface area28720 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Zinc finger protein 831
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1313
Polymers82,5232
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-16 kcal/mol
Surface area28680 Å2
MethodPISA
3
E: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: Zinc finger protein 831
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1313
Polymers82,5232
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-16 kcal/mol
Surface area28630 Å2
MethodPISA
4
G: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: Zinc finger protein 831
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1313
Polymers82,5232
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-18 kcal/mol
Surface area28770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.011, 274.011, 143.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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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.: 4
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
Zinc finger protein 831


Mass: 1548.827 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5JPB2
#3: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
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: 4.7 Å3/Da / Density % sol: 73.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.9M Ammonium Sulfate, 0.1M Tris pH=8.5, 1% Xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12717 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12717 Å / Relative weight: 1
ReflectionResolution: 3.69→137.01 Å / Num. obs: 66589 / % possible obs: 99.9 % / Redundancy: 20.7 % / CC1/2: 0.997 / Net I/σ(I): 12.1
Reflection shellResolution: 3.69→3.75 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3338 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.69→53.06 Å / SU ML: 0.4368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 3861 3.01 %
Rwork0.1976 124323 -
obs0.1989 66440 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.69→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22336 0 156 0 22492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001823016
X-RAY DIFFRACTIONf_angle_d0.444531236
X-RAY DIFFRACTIONf_chiral_restr0.03783460
X-RAY DIFFRACTIONf_plane_restr0.00414040
X-RAY DIFFRACTIONf_dihedral_angle_d4.16323048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.69-3.740.35381380.30874440X-RAY DIFFRACTION98.56
3.74-3.780.32321390.30144438X-RAY DIFFRACTION98.47
3.78-3.830.31121410.27894386X-RAY DIFFRACTION98.48
3.83-3.880.33691370.27174447X-RAY DIFFRACTION98.81
3.89-3.940.33031380.25454379X-RAY DIFFRACTION99.08
3.94-40.3041430.24414442X-RAY DIFFRACTION98.73
4-4.060.30881350.24264396X-RAY DIFFRACTION98.87
4.06-4.130.24211380.22514468X-RAY DIFFRACTION98.67
4.13-4.20.24751390.22074424X-RAY DIFFRACTION99.13
4.2-4.280.27731400.21234429X-RAY DIFFRACTION99.11
4.28-4.360.24381390.19984508X-RAY DIFFRACTION99.25
4.36-4.450.26111310.19494331X-RAY DIFFRACTION99.05
4.45-4.540.25961420.1944457X-RAY DIFFRACTION99.16
4.54-4.650.24931390.18194453X-RAY DIFFRACTION99.35
4.65-4.770.20391460.17354489X-RAY DIFFRACTION99.21
4.77-4.890.21371370.17534449X-RAY DIFFRACTION99.39
4.89-5.040.29111290.19634384X-RAY DIFFRACTION99.06
5.04-5.20.24691310.19434468X-RAY DIFFRACTION99.44
5.2-5.390.18321400.19024458X-RAY DIFFRACTION99.31
5.39-5.60.23941400.18784433X-RAY DIFFRACTION99.39
5.6-5.860.27461430.21174451X-RAY DIFFRACTION99.46
5.86-6.160.26761350.21794464X-RAY DIFFRACTION99.61
6.16-6.550.25791440.21384429X-RAY DIFFRACTION99.46
6.55-7.050.24371390.20464477X-RAY DIFFRACTION99.74
7.06-7.760.23181360.19484461X-RAY DIFFRACTION99.74
7.76-8.880.17261380.15344477X-RAY DIFFRACTION99.89
8.88-11.160.1721280.13614476X-RAY DIFFRACTION99.8
11.18-53.060.23331360.19384409X-RAY DIFFRACTION97.76

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