+Open data
-Basic information
Entry | Database: PDB / ID: 5u74 | |||||||||
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Title | Structure of human Niemann-Pick C1 protein | |||||||||
Components | Niemann-Pick C1 protein | |||||||||
Keywords | MEMBRANE PROTEIN / NPC1 | |||||||||
Function / homology | Function and homology information cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process ...cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process / cholesterol transport / programmed cell death / establishment of protein localization to membrane / adult walking behavior / lysosomal transport / cholesterol efflux / cellular response to steroid hormone stimulus / negative regulation of macroautophagy / cholesterol binding / protein glycosylation / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / negative regulation of TORC1 signaling / cholesterol metabolic process / neurogenesis / liver development / cholesterol homeostasis / macroautophagy / autophagy / endocytosis / transmembrane signaling receptor activity / late endosome membrane / nuclear envelope / virus receptor activity / signaling receptor activity / gene expression / lysosome / response to xenobiotic stimulus / symbiont entry into host cell / membrane raft / lysosomal membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.335 Å | |||||||||
Authors | Li, X. | |||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: 3.3 angstrom structure of Niemann-Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport. Authors: Li, X. / Lu, F. / Trinh, M.N. / Schmiege, P. / Seemann, J. / Wang, J. / Blobel, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u74.cif.gz | 382 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u74.ent.gz | 311.5 KB | Display | PDB format |
PDBx/mmJSON format | 5u74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u74_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5u74_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5u74_validation.xml.gz | 36 KB | Display | |
Data in CIF | 5u74_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/5u74 ftp://data.pdbj.org/pub/pdb/validation_reports/u7/5u74 | HTTPS FTP |
-Related structure data
Related structure data | 5u73C 5i31 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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1 |
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Unit cell |
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-Components
-Protein / Non-polymers , 2 types, 2 molecules A
#1: Protein | Mass: 142254.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Production host: Homo sapiens (human) / References: UniProt: O15118 |
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#6: Chemical | ChemComp-MES / |
-Sugars , 4 types, 11 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#4: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.58 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 Details: 0.1 M sodium acetate pH 5.5, 0.1 M NaCl, 10% (vol/vol) PEG4000, 6% (vol/vol) Jeffamine M-600 pH 7.0, and 6% (vol/vol) PEG P400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.335→67.919 Å / Num. obs: 30194 / % possible obs: 97.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.335→3.42 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I31 5i31 Resolution: 3.335→67.919 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.39 / 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: 3.335→67.919 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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