+Open data
-Basic information
Entry | Database: PDB / ID: 3jd8 | |||||||||
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Title | cryo-EM structure of the full-length human NPC1 at 4.4 angstrom | |||||||||
Components | Niemann-Pick C1 protein | |||||||||
Keywords | MEMBRANE PROTEIN | |||||||||
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 / lipid transporter activity / programmed cell death ...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 / lipid transporter activity / programmed cell death / bile acid metabolic process / cholesterol transport / establishment of protein localization to membrane / adult walking behavior / cellular response to low-density lipoprotein particle stimulus / lysosomal transport / cholesterol efflux / negative regulation of macroautophagy / cellular response to steroid hormone stimulus / cholesterol binding / protein glycosylation / neurogenesis / response to cadmium ion / negative regulation of TORC1 signaling / cholesterol metabolic process / liver development / cholesterol homeostasis / macroautophagy / transmembrane signaling receptor activity / autophagy / endocytosis / nuclear envelope / virus receptor activity / late endosome membrane / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.43 Å | |||||||||
Authors | Gong, X. / Qian, H.W. / Zhou, X.H. / Wu, J.P. / Zhou, Q. / Yan, N. | |||||||||
Citation | Journal: Cell / Year: 2016 Title: Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection. Authors: Xin Gong / Hongwu Qian / Xinhui Zhou / Jianping Wu / Tao Wan / Pingping Cao / Weiyun Huang / Xin Zhao / Xudong Wang / Peiyi Wang / Yi Shi / George F Gao / Qiang Zhou / Nieng Yan / Abstract: Niemann-Pick disease type C (NPC) is associated with mutations in NPC1 and NPC2, whose gene products are key players in the endosomal/lysosomal egress of low-density lipoprotein-derived cholesterol. ...Niemann-Pick disease type C (NPC) is associated with mutations in NPC1 and NPC2, whose gene products are key players in the endosomal/lysosomal egress of low-density lipoprotein-derived cholesterol. NPC1 is also the intracellular receptor for Ebola virus (EBOV). Here, we present a 4.4 Å structure of full-length human NPC1 and a low-resolution reconstruction of NPC1 in complex with the cleaved glycoprotein (GPcl) of EBOV, both determined by single-particle electron cryomicroscopy. NPC1 contains 13 transmembrane segments (TMs) and three distinct lumenal domains A (also designated NTD), C, and I. TMs 2-13 exhibit a typical resistance-nodulation-cell division fold, among which TMs 3-7 constitute the sterol-sensing domain conserved in several proteins involved in cholesterol metabolism and signaling. A trimeric EBOV-GPcl binds to one NPC1 monomer through the domain C. Our structural and biochemical characterizations provide an important framework for mechanistic understanding of NPC1-mediated intracellular cholesterol trafficking and Ebola virus infection. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jd8.cif.gz | 272 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jd8.ent.gz | 217.5 KB | Display | PDB format |
PDBx/mmJSON format | 3jd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jd8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3jd8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3jd8_validation.xml.gz | 52 KB | Display | |
Data in CIF | 3jd8_validation.cif.gz | 73.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/3jd8 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/3jd8 | HTTPS FTP |
-Related structure data
Related structure data | 6640MC 6641C 8169C 5jnxC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein / Non-polymers , 2 types, 2 molecules A
#1: Protein | Mass: 142272.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPC1 / Plasmid: pCAG / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: O15118 |
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#6: Chemical | ChemComp-CLR / |
-Sugars , 4 types, 16 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: 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 #4: 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 #5: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Niemann-Pick C1 protein / Type: COMPLEX / Synonym: NPC1 |
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Buffer solution | Name: 25mM Tris pH 8.0, 150mM NaCl and 0.1% digitonin / pH: 8 / Details: 25mM Tris pH 8.0, 150mM NaCl and 0.1% digitonin |
Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: Quantifoil R1.2/1.3 copper grid, 200 mesh |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jan 10, 2016 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 38270 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: Each micrograph | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: RELION / Resolution: 4.43 Å / Num. of particles: 102731 / Nominal pixel size: 1.30654 Å / Actual pixel size: 1.30654 Å Details: (Single particle details: Iamges were processed using RELION1.4.) (Single particle--Applied symmetry: C1) Symmetry type: POINT | ||||||||||||
Atomic model building |
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Atomic model building |
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Refinement step | Cycle: LAST
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