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- EMDB-78290: NPC1 expressed from Sf9 and purified at pH 5.5 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-78290
TitleNPC1 expressed from Sf9 and purified at pH 5.5
Map datacryoEM map of hNPC1 expressed in Sf9 and purified at pH 5.5
Sample
  • Complex: NPC1 protein
    • Protein or peptide: NPC intracellular cholesterol transporter 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Keywordstransporter / viral entry / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane raft organization / cytoplasmic side of lysosomal membrane / intracellular cholesterol transport / intracellular lipid transport / lysosome to ER cholesterol transport / negative regulation of epithelial cell apoptotic process / sterol transport / intestinal cholesterol absorption / cholesterol transport / bile acid metabolic process ...membrane raft organization / cytoplasmic side of lysosomal membrane / intracellular cholesterol transport / intracellular lipid transport / lysosome to ER cholesterol transport / negative regulation of epithelial cell apoptotic process / sterol transport / intestinal cholesterol absorption / cholesterol transport / bile acid metabolic process / LDL clearance / cholesterol transfer activity / establishment of protein localization to membrane / glycoprotein biosynthetic process / cholesterol efflux / lysosomal transport / cholesterol binding / response to cadmium ion / cholesterol homeostasis / negative regulation of TORC1 signaling / gene expression / autophagy / transmembrane signaling receptor activity / nuclear envelope / late endosome membrane / signaling receptor activity / lysosome / membrane raft / lysosomal membrane / symbiont entry into host cell / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
NPC1-like / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain
Similarity search - Domain/homology
NPC intracellular cholesterol transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWu X / Yan N
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private United States
National Science Foundation (NSF, United States)DMR-2011750 United States
CitationJournal: To Be Published
Title: Conformation switch of NPC1 epitomizes a lumen-to-membrane alternating access for nonpolar substrates
Authors: Wu X / Dehghani-Ghahnaviyeh S / Rasouli A / Malona JA / Antalek M / Jones LH / Fan X / Peng A / Tajkhorshid E / Qian H / Yan N
History
DepositionJul 25, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78290.png

Downloads & links

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Map

FileDownload / File: emd_78290.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map of hNPC1 expressed in Sf9 and purified at pH 5.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 267.36 Å		1.11 Å/pix.
x 240 pix.
= 267.36 Å		1.11 Å/pix.
x 240 pix.
= 267.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.028449405 - 0.08626217
Average (Standard dev.)-0.000022798315 (±0.0025032563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 267.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map of hNPC1 expressed in Sf9 and purified at pH 5.5

Fileemd_78290_half_map_1.map
Annotationhalf map of hNPC1 expressed in Sf9 and purified at pH 5.5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of hNPC1 expressed in Sf9 and purified at pH 5.5

Fileemd_78290_half_map_2.map
Annotationhalf map of hNPC1 expressed in Sf9 and purified at pH 5.5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NPC1 protein

EntireName: NPC1 protein
Components
  • Complex: NPC1 protein
    • Protein or peptide: NPC intracellular cholesterol transporter 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: NPC1 protein

SupramoleculeName: NPC1 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: purified from insect cell Sf9 at pH 5.5 with no additives
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NPC intracellular cholesterol transporter 1

MacromoleculeName: NPC intracellular cholesterol transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142.272906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: NPC intracellular cholesterol transporter 1

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 1 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration12 mg/mL
BufferpH: 5.5 / Component:
ConcentrationName
25.0 mMMES
150.0 mMNaCl
0.02 %GDN
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

21546

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 647158
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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