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- PDB-37lu: NPC1-NPC2 complex with bis-sterol molecule JM046, pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 37lu
TitleNPC1-NPC2 complex with bis-sterol molecule JM046, pH 5.5
Components(NPC intracellular cholesterol transporter ...) x 2
KeywordsMEMBRANE PROTEIN / transporter / complex
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
CHOLESTEROL / NPC intracellular cholesterol transporter 1 / NPC intracellular cholesterol transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWu, X. / Yan, N.
Funding support United States, 2items
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, L.H. / Fan, X. / Peng, A. / Tajkhorshid, E. / Qian, H. / Yan, N.
History
DepositionJul 25, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NPC intracellular cholesterol transporter 1
D: NPC intracellular cholesterol transporter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,97621
Polymers158,8582
Non-polymers6,11819
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, The assembly of the protein complex were determined by single-particle cryogenic electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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NPC intracellular cholesterol transporter ... , 2 types, 2 molecules AD

#1: Protein NPC intracellular cholesterol transporter 1 / Niemann-Pick C1 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 / Plasmid: pCAG / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: O15118
#2: Protein NPC intracellular cholesterol transporter 2 / Epididymal secretory protein E1 / Human epididymis-specific protein 1 / He1 / Niemann-Pick disease ...Epididymal secretory protein E1 / Human epididymis-specific protein 1 / He1 / Niemann-Pick disease type C2 protein


Mass: 16585.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPC2, HE1 / Plasmid: pCAG / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P61916

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Sugars , 3 types, 17 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of NPC1, NPC2, and bis-sterol molecule JM046 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293F / Plasmid: pCAG
Buffer solutionpH: 5.5
Buffer component
IDConc.NameBuffer-ID
125 mMMES1
2150 mMNaCl1
30.02 %GDN1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
2SerialEMimage acquisition
7Coot0.9.8.7model fitting
12RELION33D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 32074444
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66353 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 155.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003911045
ELECTRON MICROSCOPYf_angle_d0.794115053
ELECTRON MICROSCOPYf_chiral_restr0.05161772
ELECTRON MICROSCOPYf_plane_restr0.00561882
ELECTRON MICROSCOPYf_dihedral_angle_d11.5731591

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