5JNX

The 6.6 A cryo-EM structure of the full-length human NPC1 in complex with the cleaved glycoprotein of Ebola virus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into the Niemann-Pick C1 (NPC1)-Mediated Cholesterol Transfer and Ebola Infection

Gong, X.Qian, H.Zhou, X.Wu, J.Wan, T.Cao, P.Huang, W.Zhao, X.Wang, X.Wang, P.Shi, Y.Gao, G.F.Zhou, Q.Yan, N.

(2016) Cell 165: 1467-1478

  • DOI: 10.1016/j.cell.2016.05.022

  • PubMed Abstract: 
  • Niemann-Pick disease type C (NPC) is associated with mutations in NPC1 and NPC2, whose gene products are key players in the endosomal/lysosomal egress of low-density lipoprotein-derived cholesterol. NPC1 is also the intracellular receptor for Ebola v ...

    Niemann-Pick disease type C (NPC) is associated with mutations in NPC1 and NPC2, whose gene products are key players in the endosomal/lysosomal egress of low-density lipoprotein-derived cholesterol. NPC1 is also the intracellular receptor for Ebola virus (EBOV). Here, we present a 4.4 Å structure of full-length human NPC1 and a low-resolution reconstruction of NPC1 in complex with the cleaved glycoprotein (GPcl) of EBOV, both determined by single-particle electron cryomicroscopy. NPC1 contains 13 transmembrane segments (TMs) and three distinct lumenal domains A (also designated NTD), C, and I. TMs 2-13 exhibit a typical resistance-nodulation-cell division fold, among which TMs 3-7 constitute the sterol-sensing domain conserved in several proteins involved in cholesterol metabolism and signaling. A trimeric EBOV-GPcl binds to one NPC1 monomer through the domain C. Our structural and biochemical characterizations provide an important framework for mechanistic understanding of NPC1-mediated intracellular cholesterol trafficking and Ebola virus infection.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Niemann-Pick C1 protein
A
1278Homo sapiensMutation(s): 0 
Gene Names: NPC1
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sterol-Sensing Domain (SSD) Proteins
Protein: 
Niemann-Pick C1 protein (NPC1*)
Find proteins for O15118 (Homo sapiens)
Go to Gene View: NPC1
Go to UniProtKB:  O15118
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
C, E, G
158Zaire ebolavirus (strain Kikwit-95)Mutation(s): 1 
Gene Names: GP
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sterol-Sensing Domain (SSD) Proteins
Protein: 
Niemann-Pick C1 protein (NPC1*)
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Go to UniProtKB:  P87666
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein
D, F, H
130Zaire ebolavirus (strain Kikwit-95)Mutation(s): 0 
Gene Names: GP
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Sterol-Sensing Domain (SSD) Proteins
Protein: 
Niemann-Pick C1 protein (NPC1*)
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Go to UniProtKB:  P87666
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D, F, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2015CB9101012014, ZX09507003006
National Natural Science Foundation of ChinaChinaproject 31321062 and 81590761
President Foundation of Chinese Academy of Sciences and Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08020100

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Data processing, Database references