Cryo_EM structure of delta N-NPC1L1-EZE

Experimental Data Snapshot

  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Structural insights into the mechanism of human NPC1L1-mediated cholesterol uptake.

Hu, M.Yang, F.Huang, Y.You, X.Liu, D.Sun, S.Sui, S.F.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abg3188
  • Primary Citation of Related Structures:  
    7DF8, 7DFW, 7DFZ

  • PubMed Abstract: 

    Niemann-Pick C1-like 1 (NPC1L1) protein plays a central role in the intestinal cholesterol absorption and is the target of a drug, ezetimibe, which inhibits NPC1L1 to reduce cholesterol absorption. Here, we present cryo-electron microscopy structures of human NPC1L1 in apo state, cholesterol-enriched state, and ezetimibe-bound state to reveal molecular details of NPC1L1-mediated cholesterol uptake and ezetimibe inhibition. Comparison of these structures reveals that the sterol-sensing domain (SSD) could respond to the cholesterol level alteration by binding different number of cholesterol molecules. Upon increasing cholesterol level, SSD binds more cholesterol molecules, which, in turn, triggers the formation of a stable structural cluster in SSD, while binding of ezetimibe causes the deformation of the SSD and destroys the structural cluster, leading to the inhibition of NPC1L1 function. These results provide insights into mechanisms of NPC1L1 function and ezetimibe action and are of great significance for the development of new cholesterol absorption inhibitors.

  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NPC1-like intracellular cholesterol transporter 11,273Homo sapiensMutation(s): 0 
Gene Names: NPC1L1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHC9 (Homo sapiens)
Explore Q9UHC9 
Go to UniProtKB:  Q9UHC9
GTEx:  ENSG00000015520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHC9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth E],
E [auth P]
Glycosylation Resources
GlyTouCan:  G11411VI
GlyCosmos:  G11411VI
GlyGen:  G11411VI
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth H]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79924RM
GlyCosmos:  G79924RM
GlyGen:  G79924RM
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth J],
F [auth T]
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H56 (Subject of Investigation/LOI)
Query on H56

Download Ideal Coordinates CCD File 
L [auth A](3~{R},4~{S})-1-(4-fluorophenyl)-3-[(3~{S})-3-(4-fluorophenyl)-3-oxidanyl-propyl]-4-(4-hydroxyphenyl)azetidin-2-one
C24 H21 F2 N O3
Query on CLR

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
O [auth A],
P [auth A]
C27 H46 O
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2021-08-11 
  • Deposition Author(s): Hu, M., Sun, S.

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release