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Yorodumi- PDB-5jnx: The 6.6 A cryo-EM structure of the full-length human NPC1 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jnx | ||||||||||||
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Title | The 6.6 A cryo-EM structure of the full-length human NPC1 in complex with the cleaved glycoprotein of Ebola virus | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / protein complex | ||||||||||||
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 / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / lysosome / symbiont-mediated suppression of host innate immune response / response to xenobiotic stimulus / symbiont entry into host cell / membrane raft / lysosomal membrane / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / perinuclear region of cytoplasm / host cell plasma membrane / virion membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Ebola virus - Zaire | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.56 Å | ||||||||||||
Authors | Gong, X. / Qian, H.W. / Zhou, X.H. / Wu, J.P. / Wan, T. / Shi, Y. / Gao, F. / Zhou, Q. / Yan, N. | ||||||||||||
Funding support | China, 3items
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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 | 5jnx.cif.gz | 554.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jnx.ent.gz | 466.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jnx_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5jnx_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5jnx_validation.xml.gz | 70.4 KB | Display | |
Data in CIF | 5jnx_validation.cif.gz | 100 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/5jnx ftp://data.pdbj.org/pub/pdb/validation_reports/jn/5jnx | HTTPS FTP |
-Related structure data
Related structure data | 8169MC 6640C 6641C 3jd8C 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 , 3 types, 7 molecules ACEGDFH
#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 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: O15118 | ||
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#2: Protein | Mass: 17194.543 Da / Num. of mol.: 3 / Fragment: UNP residues 32-188 / Mutation: T42V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus - Zaire (1995) / Gene: GP / Cell line (production host): Hi-5 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P87666 #3: Protein | Mass: 14882.807 Da / Num. of mol.: 3 / Fragment: UNP residues 509-632 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ebola virus - Zaire (1995) / Gene: GP / Cell line (production host): Hi-5 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P87666 |
-Sugars , 4 types, 18 molecules
#4: 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 #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 #6: 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 #7: 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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Conc.: 15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 25 mM Tris pH 8.0, 150 mM NaCl and 0.1% digitonin | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
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: 2700 nm / Nominal defocus min: 1700 nm / Calibrated defocus min: 1700 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 105 K / Temperature (min): 80 K |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1379 |
Image scans | Sampling size: 5 µm / Movie frames/image: 32 / Used frames/image: 0-32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 703336 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50223 / Symmetry type: POINT |