+Open data
-Basic information
Entry | Database: PDB / ID: 5lwv | ||||||
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Title | Human OGT in complex with UDP and fused substrate peptide (HCF1) | ||||||
Components | Host cell factor 1,UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | ||||||
Keywords | TRANSFERASE / glycosylation / signalling / O-GlcNAc / O-GlcNAc transferase / substrate recognition | ||||||
Function / homology | Function and homology information protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / release from viral latency / 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 N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / release from viral latency / 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 / Set1C/COMPASS complex / MLL1/2 complex / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / histone methyltransferase complex / 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 / MLL1 complex / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / regulation of protein-containing complex assembly / positive regulation of cell cycle / 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 / Transcriptional activation of mitochondrial biogenesis / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / protein-macromolecule adaptor activity / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / protein stabilization / chromatin remodeling / cadherin binding / cell cycle / neuronal cell body / glutamatergic synapse / apoptotic process / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / 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 / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Raimi, O. / Rafie, K. / Kapuria, V. / Herr, W. / van Aalten, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biol / Year: 2017 Title: Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats. Authors: Rafie, K. / Raimi, O. / Ferenbach, A.T. / Borodkin, V.S. / Kapuria, V. / van Aalten, D.M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lwv.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lwv.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 5lwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lwv ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lwv | HTTPS FTP |
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-Related structure data
Related structure data | 5lvvC 3pe4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 83779.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HCFC1, HCF1, HFC1, OGT / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P51610, UniProt: O15294, protein O-GlcNAc transferase | ||
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#2: Chemical | ChemComp-UDP / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.3M Ammonium tartrate diabasic; 0.1M Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2015 / Details: Toroidal mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.53 Å / Num. obs: 106157 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rsym value: 0.12 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.95 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.684 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PE4 Resolution: 1.9→48.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.731 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.491 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.5 Å
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