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Yorodumi- PDB-5lev: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lev | ||||||
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Title | Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) | ||||||
Components | UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase | ||||||
Keywords | TRANSFERASE / Protein glycosylation / integral membrane protein / congenital myasthenic syndrome 13 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle ...Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein / Defective DPAGT1 causes CDG-1j, CMSTA2 / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase / UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity / UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity / dolichol-linked oligosaccharide biosynthetic process / UDP-N-acetylglucosamine metabolic process / protein N-linked glycosylation / glycosyltransferase activity / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / identical protein binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Pike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. ...Pike, A.C.W. / Dong, Y.Y. / Chu, A. / Tessitore, A. / Goubin, S. / Dong, L. / Mukhopadhyay, S. / Mahajan, P. / Chalk, R. / Berridge, G. / Wang, D. / Kupinska, K. / Belaya, K. / Beeson, D. / Burgess-Brown, N. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Cell / Year: 2018 Title: Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design. Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / ...Authors: Dong, Y.Y. / Wang, H. / Pike, A.C.W. / Cochrane, S.A. / Hamedzadeh, S. / Wyszynski, F.J. / Bushell, S.R. / Royer, S.F. / Widdick, D.A. / Sajid, A. / Boshoff, H.I. / Park, Y. / Lucas, R. / Liu, W.M. / Lee, S.S. / Machida, T. / Minall, L. / Mehmood, S. / Belaya, K. / Liu, W.W. / Chu, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Strain-Damerell, C. / Chalk, R. / Burgess-Brown, N.A. / Bibb, M.J. / Barry Iii, C.E. / Robinson, C.V. / Beeson, D. / Davis, B.G. / Carpenter, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lev.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lev.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lev_validation.pdf.gz | 543.7 KB | Display | wwPDB validaton report |
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Full document | 5lev_full_validation.pdf.gz | 548.8 KB | Display | |
Data in XML | 5lev_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 5lev_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/5lev ftp://data.pdbj.org/pub/pdb/validation_reports/le/5lev | HTTPS FTP |
-Related structure data
Related structure data | 5o5eC 6fm9C 6fwzC 4j72S 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: 46173.719 Da / Num. of mol.: 1 / Mutation: V264G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPAGT1, DPAGT2 / Plasmid: pFB-LIC-Bse / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9H3H5, UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase |
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#2: Chemical | ChemComp-UNL / Mass: 790.145 Da / Num. of mol.: 1 Fragment: RESIDUE UNL 501 REPRESENTS AN UNIDENTIFIED LIPID BOUND TO THE TMD AND IS PRESENT IN ALL DPAGT1 DATASETS ANALYSED Source method: obtained synthetically |
#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: 3.99 Å3/Da / Density % sol: 69.18 % Preparation: EXPERIMENTAL DATA STATISTICS REPORTED ARE THOSE PRIOR TO ANISOTROPIC DATA TRUNCATION WITH STARANISO |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M bicine pH 9.0, 0.05M sodium chloride, 38% PEG300, 5mM Na2WO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→59.79 Å / Num. obs: 13206 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 120.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.36 / CC1/2: 0.549 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J72 Resolution: 3.2→26.71 Å / Cor.coef. Fo:Fc: 0.8965 / Cor.coef. Fo:Fc free: 0.9095 / SU R Cruickshank DPI: 1.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.362 / SU Rfree Blow DPI: 0.366 / SU Rfree Cruickshank DPI: 0.365 Details: Data were scaled with Aimless and then anisotropically truncated with STARANISO. Structure refined with BUSTER with a single TLS group. Electron density maps were sharpened with -100A**2 ...Details: Data were scaled with Aimless and then anisotropically truncated with STARANISO. Structure refined with BUSTER with a single TLS group. Electron density maps were sharpened with -100A**2 bfactor for rebuilding in COOT.
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Displacement parameters | Biso mean: 142.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.438 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→26.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.5 Å / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 46.1881 Å / Origin y: 50.2503 Å / Origin z: 128.211 Å
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Refinement TLS group | Selection details: {A|8 - 403} |