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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21548 | |||||||||
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Title | NPC1 structure in GDN micelles at pH 5.5, conformation b | |||||||||
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Function / homology | ![]() 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 / lysosomal transport / cholesterol efflux / negative regulation of macroautophagy / cellular response to steroid hormone stimulus / 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 / nuclear envelope / late endosome membrane / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Yan N / Qian HW / Wu XL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Low-pH-Dependent Lysosomal Cholesterol Egress by NPC1 and NPC2. Authors: Hongwu Qian / Xuelan Wu / Ximing Du / Xia Yao / Xin Zhao / Joyce Lee / Hongyuan Yang / Nieng Yan / ![]() ![]() ![]() Abstract: Lysosomal cholesterol egress requires two proteins, NPC1 and NPC2, whose defects are responsible for Niemann-Pick disease type C (NPC). Here, we present systematic structural characterizations that ...Lysosomal cholesterol egress requires two proteins, NPC1 and NPC2, whose defects are responsible for Niemann-Pick disease type C (NPC). Here, we present systematic structural characterizations that reveal the molecular basis for low-pH-dependent cholesterol delivery from NPC2 to the transmembrane (TM) domain of NPC1. At pH 8.0, similar structures of NPC1 were obtained in nanodiscs and in detergent at resolutions of 3.6 Å and 3.0 Å, respectively. A tunnel connecting the N-terminal domain (NTD) and the transmembrane sterol-sensing domain (SSD) was unveiled. At pH 5.5, the NTD exhibits two conformations, suggesting the motion for cholesterol delivery to the tunnel. A putative cholesterol molecule is found at the membrane boundary of the tunnel, and TM2 moves toward formation of a surface pocket on the SSD. Finally, the structure of the NPC1-NPC2 complex at 4.0 Å resolution was obtained at pH 5.5, elucidating the molecular basis for cholesterol handoff from NPC2 to NPC1(NTD). | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.6 KB 12.6 KB | Display Display | ![]() |
Images | ![]() | 107.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w5uMC ![]() 6w5rC ![]() 6w5sC ![]() 6w5tC ![]() 6w5vC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.114 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : NPC1 in GDN micelles at pH 5.5
Entire | Name: NPC1 in GDN micelles at pH 5.5 |
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Components |
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-Supramolecule #1: NPC1 in GDN micelles at pH 5.5
Supramolecule | Name: NPC1 in GDN micelles at pH 5.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: NPC intracellular cholesterol transporter 1
Macromolecule | Name: NPC intracellular cholesterol transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 146.083688 KDa |
Recombinant expression | Organism: ![]() |
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 LNFLE GSDE VDAGSHHHHH HHHHHGSVED YKDDDDK |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #6: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 2 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Software - Name: Gctf |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 169487 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |