+Open data
-Basic information
Entry | Database: PDB / ID: 5hns | |||||||||
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Title | Structure of glycosylated NPC1 luminal domain C | |||||||||
Components | Niemann-Pick C1 protein | |||||||||
Keywords | PROTEIN BINDING / Niemann-Pick disease type C / NPC1 / NPC2 / cholesterol transport / Ebola virus receptor / Ebola virus susceptibility | |||||||||
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 / SAD / Resolution: 2.45 Å | |||||||||
Authors | Zhao, Y. / Ren, J. / Harlos, K. / Stuart, D.I. | |||||||||
Citation | Journal: Febs Lett. / Year: 2016 Title: Structure of glycosylated NPC1 luminal domain C reveals insights into NPC2 and Ebola virus interactions. Authors: Zhao, Y. / Ren, J. / Harlos, K. / Stuart, D.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hns.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hns.ent.gz | 164 KB | Display | PDB format |
PDBx/mmJSON format | 5hns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hns_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5hns_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 5hns_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5hns_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hns ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hns | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27952.037 Da / Num. of mol.: 2 / Fragment: domain C, UNP residues 387-618 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Cell line (production host): HEK293S / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: O15118 |
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-Sugars , 5 types, 9 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Organ (production host): kidney / Production host: Homo sapiens (human) #3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Organ (production host): kidney / Production host: Homo sapiens (human) #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Organ (production host): kidney / Production host: Homo sapiens (human) #6: Sugar | ChemComp-NAG / | Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Organ (production host): kidney / Production host: Homo sapiens (human) |
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-Non-polymers , 2 types, 48 molecules
#7: Chemical | ChemComp-SCN / #8: 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: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 30% polyethylene glycol mono-ethyl Ether 2000 and 0.1 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0675 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0675 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→70 Å / Num. obs: 28062 / % possible obs: 100 % / Redundancy: 26.5 % / Net I/σ(I): 13.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→70.03 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.941 / SU B: 21.463 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.228 / 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: 73.014 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→70.03 Å
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