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 2.1 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: https://doi.org/10.1016/j.cell.2016.05.022
  • Primary Citation of Related Structures:  
    5JNX

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Niemann-Pick C1 protein1,278Homo sapiensMutation(s): 0 
Gene Names: NPC1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15118 (Homo sapiens)
Explore O15118 
Go to UniProtKB:  O15118
PHAROS:  O15118
GTEx:  ENSG00000141458 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15118
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinB [auth C],
D [auth E],
F [auth G]
158Ebola virus - Zaire (1995)Mutation(s): 1 
Gene Names: GP
Membrane Entity: Yes 
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Explore P87666 
Go to UniProtKB:  P87666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP87666
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoproteinC [auth D],
E [auth F],
G [auth H]
130Ebola virus - Zaire (1995)Mutation(s): 0 
Gene Names: GP
Membrane Entity: Yes 
UniProt
Find proteins for P87666 (Zaire ebolavirus (strain Kikwit-95))
Explore P87666 
Go to UniProtKB:  P87666
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP87666
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H [auth B],
I,
K,
M,
N,
H [auth B],
I,
K,
M,
N,
O,
P
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.56 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Data processing, Database references
  • Version 1.2: 2019-10-23
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Data collection
  • Version 1.4: 2019-12-11
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2020-08-05
    Changes: Derived calculations, Source and taxonomy, Structure summary