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Yorodumi- PDB-5kij: Crystal structure of the class I human endoplasmic reticulum 1,2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kij | |||||||||||||||
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Title | Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex | |||||||||||||||
Components | Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase | |||||||||||||||
Keywords | HYDROLASE / alpha/alpha-barrel / cation replacement / protein-glycan interaction | |||||||||||||||
Function / homology | Function and homology information mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / : / protein glycosylation / ERAD pathway ...mannoprotein catabolic process / Defective MAN1B1 causes MRT15 / protein alpha-1,2-demannosylation / mannosyl-oligosaccharide 1,2-alpha-mannosidase / mannosyl-oligosaccharide 1,2-alpha-mannosidase activity / endoplasmic reticulum quality control compartment / oligosaccharide metabolic process / : / protein glycosylation / ERAD pathway / ER Quality Control Compartment (ERQC) / extracellular vesicle / cytoplasmic vesicle / Maturation of spike protein / viral protein processing / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å | |||||||||||||||
Authors | Karaveg, K. / Xiang, Y. / Moremen, K.W. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016 Title: Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway. Authors: Xiang, Y. / Karaveg, K. / Moremen, K.W. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kij.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kij.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 5kij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/5kij ftp://data.pdbj.org/pub/pdb/validation_reports/ki/5kij | HTTPS FTP |
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-Related structure data
Related structure data | 5kk7C 5kkbC 1x9dS 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 52030.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAN1B1, UNQ747/PRO1477 / Production host: Komagataella pastoris (fungus) References: UniProt: Q9UKM7, mannosyl-oligosaccharide 1,2-alpha-mannosidase |
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#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 613 molecules
#3: Chemical | ChemComp-LA / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-BU1 / #6: Chemical | ChemComp-1PS / | #7: 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: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24% PEG 4000, 50mM ammonium sulfate, 0.1M MES, 10% 1,4-butanediol, pH 6.5, 200mM NDSB-200, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→48.69 Å / Num. obs: 53113 / % possible obs: 96.5 % / Redundancy: 1.9 % / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.649→1.691 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1X9D Resolution: 1.649→27.081 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 2.03 / Phase error: 23.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.649→27.081 Å
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Refine LS restraints |
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LS refinement shell |
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