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- EMDB-78289: NPC1-NPC2 complex with bis-sterol molecule JM046, pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-78289
TitleNPC1-NPC2 complex with bis-sterol molecule JM046, pH 5.5
Map datacryoEM map of NPC1-NPC2 complex with bis-sterol compound JM046, pH 5.5
Sample
  • Complex: Complex of NPC1, NPC2, and bis-sterol molecule JM046
    • Protein or peptide: NPC intracellular cholesterol transporter 1
    • Protein or peptide: NPC intracellular cholesterol transporter 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
Keywordstransporter / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of isoprenoid metabolic process / glycolipid transport / intracellular sterol transport / 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 ...regulation of isoprenoid metabolic process / glycolipid transport / intracellular sterol transport / 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 / phospholipid transport / cholesterol transfer activity / establishment of protein localization to membrane / glycoprotein biosynthetic process / cholesterol efflux / lysosomal transport / cholesterol binding / cholesterol metabolic process / response to cadmium ion / cholesterol homeostasis / lysosomal lumen / negative regulation of TORC1 signaling / gene expression / autophagy / response to virus / azurophil granule lumen / transmembrane signaling receptor activity / late endosome / nuclear envelope / late endosome membrane / signaling receptor activity / lysosome / membrane raft / lysosomal membrane / symbiont entry into host cell / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / endoplasmic reticulum / : / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Npc2 like, ML domain / Sterol transport protein NPC2-like / NPC1-like / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain ...Npc2 like, ML domain / Sterol transport protein NPC2-like / NPC1-like / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / 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 / Immunoglobulin E-set
Similarity search - Domain/homology
NPC intracellular cholesterol transporter 1 / NPC intracellular cholesterol transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 J / 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_78289.png

Downloads & links

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Map

FileDownload / File: emd_78289.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM map of NPC1-NPC2 complex with bis-sterol compound JM046, 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: 0.012
Minimum - Maximum-0.049987894 - 0.11674914
Average (Standard dev.)0.000007587197 (±0.0031094966)
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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Additional map: focus-refined map of NPC1-NPC2 complex with bis-sterol compound...

Fileemd_78289_additional_1.map
Annotationfocus-refined map of NPC1-NPC2 complex with bis-sterol compound JM046 at ECD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of NPC1-NPC2 complex with bis-sterol compound JM046, pH 5.5

Fileemd_78289_half_map_1.map
Annotationhalf map of NPC1-NPC2 complex with bis-sterol compound JM046, 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 NPC1-NPC2 complex with bis-sterol compound JM046, pH 5.5

Fileemd_78289_half_map_2.map
Annotationhalf map of NPC1-NPC2 complex with bis-sterol compound JM046, 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 : Complex of NPC1, NPC2, and bis-sterol molecule JM046

EntireName: Complex of NPC1, NPC2, and bis-sterol molecule JM046
Components
  • Complex: Complex of NPC1, NPC2, and bis-sterol molecule JM046
    • Protein or peptide: NPC intracellular cholesterol transporter 1
    • Protein or peptide: NPC intracellular cholesterol transporter 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL

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Supramolecule #1: Complex of NPC1, NPC2, and bis-sterol molecule JM046

SupramoleculeName: Complex of NPC1, NPC2, and bis-sterol molecule JM046 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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 #2: NPC intracellular cholesterol transporter 2

MacromoleculeName: NPC intracellular cholesterol transporter 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.585152 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MRFLAATFLL LALSTAAQAE PVQFKDCGSV DGVIKEVNVS PCPTQPCQLS KGQSYSVNVT FTSNIQSKSS KAVVHGILMG VPVPFPIPE PDGCKSGINC PIQKDKTYSY LNKLPVKSEY PSIKLVVEWQ LQDDKNQSLF CWEIPVQIVS HL

UniProtKB: NPC intracellular cholesterol transporter 2

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

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

Particle selectionNumber selected: 32074444
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6w5v

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 66353
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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