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Yorodumi- EMDB-8169: cryo-EM map of the full-length human NPC1 in complex with the cle... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8169 | ||||||||||||||||||
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Title | cryo-EM map of the full-length human NPC1 in complex with the cleaved glycoprotein of Ebola virus | ||||||||||||||||||
Map data | None | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intestinal cholesterol absorption / LDL clearance / cholesterol efflux / programmed cell death / negative regulation of epithelial cell apoptotic process ...cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intestinal cholesterol absorption / LDL clearance / cholesterol efflux / programmed cell death / negative regulation of epithelial cell apoptotic process / cholesterol transport / bile acid metabolic process / establishment of protein localization to membrane / adult walking behavior / lysosomal transport / cholesterol binding / negative regulation of macroautophagy / cellular response to steroid hormone stimulus / protein glycosylation / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / negative regulation of TORC1 signaling / cholesterol metabolic process / neurogenesis / cholesterol homeostasis / liver development / macroautophagy / autophagy / endocytosis / transmembrane signaling receptor activity / virus receptor activity / gene expression / signaling receptor activity / nuclear envelope / late endosome membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / lysosome / response to xenobiotic stimulus / symbiont entry into host cell / membrane raft / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion 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 | single particle reconstruction / cryo EM / Resolution: 6.56 Å | ||||||||||||||||||
Authors | Yan N / Zhou Q / Gong X / Qiang HW / Zhou XH / Wu JP / Gao F / Wan T / Shi Y | ||||||||||||||||||
Funding support | China, 5 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8169.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-8169-v30.xml emd-8169.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_8169.png | 58.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8169 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8169 | HTTPS FTP |
-Related structure data
Related structure data | 5jnxMC 6640C 6641C 3jd8C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8169.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.30654 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : NPC1 in complex with EBOV-GPcl trimer
Entire | Name: NPC1 in complex with EBOV-GPcl trimer |
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Components |
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-Supramolecule #1: NPC1 in complex with EBOV-GPcl trimer
Supramolecule | Name: NPC1 in complex with EBOV-GPcl trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) / Organ: lysosome |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant plasmid: pCAG |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: NPC1 in complex with EBOV-GPcl trimer
Macromolecule | Name: NPC1 in complex with EBOV-GPcl trimer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTARGLALGL LLLLLCPAQV FSQSCVWYGE CGIAYGDKRY NCEYSGPPKP LPKDGYDLVQ ELCPGFFFGN VSLCCDVRQL QTLKDNLQL PLQFLSRCPS CFYNLLNLFC ELTCSPRQSQ FLNVTATEDY VDPVTNQTKT NVKELQYYVG QSFANAMYNA C RDVEAPSS ...String: MTARGLALGL LLLLLCPAQV FSQSCVWYGE CGIAYGDKRY NCEYSGPPKP LPKDGYDLVQ ELCPGFFFGN VSLCCDVRQL QTLKDNLQL PLQFLSRCPS CFYNLLNLFC ELTCSPRQSQ FLNVTATEDY VDPVTNQTKT NVKELQYYVG QSFANAMYNA C RDVEAPSS NDKALGLLCG KDADACNATN WIEYMFNKDN GQAPFTITPV FSDFPVHGME PMNNATKGCD ESVDEVTAPC SC QDCSIVC GPKPQPPPPP APWTILGLDA MYVIMWITYM AFLLVFFGAF FAVWCYRKRY FVSEYTPIDS NIAFSVNASD KGE ASCCDP VSAAFEGCLR RLFTRWGSFC VRNPGCVIFF SLVFITACSS GLVFVRVTTN PVDLWSAPSS QARLEKEYFD QHFG PFFRT EQLIIRAPLT DKHIYQPYPS GADVPFGPPL DIQILHQVLD LQIAIENITA SYDNETVTLQ DICLAPLSPY NTNCT ILSV LNYFQNSHSV LDHKKGDDFF VYADYHTHFL YCVRAPASLN DTSLLHDPCL GTFGGPVFPW LVLGGYDDQN YNNATA LVI TFPVNNYYND TEKLQRAQAW EKEFINFVKN YKNPNLTISF TAERSIEDEL NRESDSDVFT VVISYAIMFL YISLALG HM KSCRRLLVDS KVSLGIAGIL IVLSSVACSL GVFSYIGLPL TLIVIEVIPF LVLAVGVDNI FILVQAYQRD ERLQGETL D QQLGRVLGEV APSMFLSSFS ETVAFFLGAL SVMPAVHTFS LFAGLAVFID FLLQITCFVS LLGLDIKRQE KNRLDIFCC VRGAEDGTSV QASESCLFRF FKNSYSPLLL KDWMRPIVIA IFVGVLSFSI AVLNKVDIGL DQSLSMPDDS YMVDYFKSIS QYLHAGPPV YFVLEEGHDY TSSKGQNMVC GGMGCNNDSL VQQIFNAAQL DNYTRIGFAP SSWIDDYFDW VKPQSSCCRV D NITDQFCN ASVVDPACVR CRPLTPEGKQ RPQGGDFMRF LPMFLSDNPN PKCGKGGHAA YSSAVNILLG HGTRVGATYF MT YHTVLQT SADFIDALKK ARLIASNVTE TMGINGSAYR VFPYSVFYVF YEQYLTIIDD TIFNLGVSLG AIFLVTMVLL GCE LWSAVI MCATIAMVLV NMFGVMWLWG ISLNAVSLVN LVMSCGISVE FCSHITRAFT VSMKGSRVER AEEALAHMGS SVFS GITLT KFGGIVVLAF AKSQIFQIFY FRMYLAMVLL GATHGLIFLP VLLSYIGPSV NKAKSCATEE RYKGTERERL LNF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 5.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.7 µm / Calibrated defocus min: 1.7 µm / Calibrated magnification: 38270 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 22500 |
Specialist optics | Spherical aberration corrector: no / Chromatic aberration corrector: no / Energy filter - Name: no |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-32 / Number real images: 1379 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 703336 |
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CTF correction | Software - Name: Gctf (ver. 0.38) |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 50223 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-5jnx: |