+Open data
-Basic information
Entry | Database: PDB / ID: 4m92 | ||||||
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Title | Crystal structure of hN33/Tusc3-peptide 2 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / thioredoxin-like fold / thiol/disulfide oxidoreductase / thiol/disulfide exchange reactions / redox-active protein | ||||||
Function / homology | Function and homology information trans-synaptic signaling by trans-synaptic complex / Asparagine N-linked glycosylation / Interleukin-38 signaling / Receptor-type tyrosine-protein phosphatases / magnesium ion transport / presynaptic membrane assembly / oligosaccharyltransferase complex / Miscellaneous transport and binding events / protein N-linked glycosylation via asparagine / magnesium ion transmembrane transporter activity ...trans-synaptic signaling by trans-synaptic complex / Asparagine N-linked glycosylation / Interleukin-38 signaling / Receptor-type tyrosine-protein phosphatases / magnesium ion transport / presynaptic membrane assembly / oligosaccharyltransferase complex / Miscellaneous transport and binding events / protein N-linked glycosylation via asparagine / magnesium ion transmembrane transporter activity / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / protein N-linked glycosylation / negative regulation of exocytosis / positive regulation of synapse assembly / positive regulation of dendrite morphogenesis / regulation of postsynapse organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly / transmembrane transport / neuron differentiation / cognition / postsynaptic membrane / Maturation of spike protein / axon / signaling receptor binding / dendrite / glutamatergic synapse / endoplasmic reticulum membrane / cell surface / signal transduction / mitochondrion / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural basis of substrate specificity of human oligosaccharyl transferase subunit n33/tusc3 and its role in regulating protein N-glycosylation. Authors: Mohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m92.cif.gz | 53.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m92.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 4m92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m92 ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m92 | HTTPS FTP |
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-Related structure data
Related structure data | 4m8gSC 4m90C 4m91C 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
#1: Protein | Mass: 19125.799 Da / Num. of mol.: 1 / Fragment: unp residues 44-194 / Mutation: C123S, C102S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUSC3, N33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13454 |
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#2: Protein/peptide | Mass: 1834.960 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 207-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAPL1, OPHN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZN1 |
#3: 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: 1.91 Å3/Da / Density % sol: 35.6 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25.1 Å / Num. all: 21798 / Num. obs: 21733 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.637 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.7.0032 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4M8G Resolution: 1.6→25.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.026 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.668 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25.09 Å
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