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Yorodumi- PDB-5ggp: Crystal structure of N-terminal domain of human protein O-mannose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ggp | |||||||||
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Title | Crystal structure of N-terminal domain of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with GlcNAc-beta1,2-Man-peptide | |||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / glycosyltransferease / O-mannosylation / alpha-dystroglycan | |||||||||
Function / homology | Function and homology information Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of embryonic cell shape ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / dystroglycan complex / nerve maturation / beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity / muscle attachment / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / positive regulation of basement membrane assembly involved in embryonic body morphogenesis / retrograde trans-synaptic signaling by trans-synaptic protein complex / regulation of embryonic cell shape / O-linked glycosylation / contractile ring / localization of cell / dystrophin-associated glycoprotein complex / regulation of gastrulation / microtubule anchoring / calcium-dependent cell-matrix adhesion / morphogenesis of an epithelial sheet / reactive gliosis / protein O-linked mannosylation / laminin-1 binding / O-glycan processing / response to denervation involved in regulation of muscle adaptation / acetylglucosaminyltransferase activity / basement membrane organization / positive regulation of myelination / dystroglycan binding / regulation of epithelial to mesenchymal transition / photoreceptor ribbon synapse / skeletal muscle tissue regeneration / vinculin binding / cellular response to cholesterol / nerve development / myelination in peripheral nervous system / EGR2 and SOX10-mediated initiation of Schwann cell myelination / branching involved in salivary gland morphogenesis / costamere / dentate gyrus development / protein O-linked glycosylation / node of Ranvier / commissural neuron axon guidance / angiogenesis involved in wound healing / response to muscle activity / structural constituent of muscle / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / axon regeneration / postsynaptic cytosol / positive regulation of cell-matrix adhesion / Transferases; Glycosyltransferases; Hexosyltransferases / epithelial tube branching involved in lung morphogenesis / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / negative regulation of MAPK cascade / alpha-actinin binding / plasma membrane raft / membrane protein ectodomain proteolysis / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GABA-ergic synapse / ECM proteoglycans / laminin binding / heart morphogenesis / myelination / SH2 domain binding / nuclear periphery / tubulin binding / negative regulation of cell migration / filopodium / axon guidance / morphogenesis of an epithelium / sensory perception of sound / adherens junction / regulation of synaptic plasticity / sarcolemma / response to peptide hormone / Regulation of expression of SLITs and ROBOs / Golgi lumen / cellular response to mechanical stimulus / protein transport / virus receptor activity / lamellipodium / gene expression / actin binding / manganese ion binding / postsynaptic membrane / carbohydrate binding / basolateral plasma membrane / collagen-containing extracellular matrix / cytoskeleton / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / protein-containing complex binding / extracellular space / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å | |||||||||
Authors | Kuwabara, N. / Senda, T. / Kato, R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of alpha-dystroglycan Authors: Kuwabara, N. / Manya, H. / Yamada, T. / Tateno, H. / Kanagawa, M. / Kobayashi, K. / Akasaka-Manya, K. / Hirose, Y. / Mizuno, M. / Ikeguchi, M. / Toda, T. / Hirabayashi, J. / Senda, T. / Endo, T. / Kato, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ggp.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ggp.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ggp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggp ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggp | HTTPS FTP |
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-Related structure data
Related structure data | 5ggfC 5gggSC 5ggiC 5ggjC 5ggkC 5gglC 5ggnC 5ggoC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17623.020 Da / Num. of mol.: 2 / Fragment: UNP residues 92-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475 / Production host: Escherichia coli (E. coli) References: UniProt: Q8WZA1, Transferases; Glycosyltransferases; Hexosyltransferases #2: Protein/peptide | Mass: 927.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14118 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES-NaOH, LiCl2, Na acetate, PEG-6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.599→46.6 Å / Num. obs: 78168 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.5 / % possible all: 95.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GGG Resolution: 1.599→46.554 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.77 Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.599→46.554 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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