8EUS | pdb_00008eus

Crystal structure of NPC1 luminal domain C

• PDB DOI: https://doi.org/10.2210/pdb8EUS/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2022-10-19 Released: 2023-02-22 
• Deposition Author(s): Odongo, L., Pornillos, O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Purification and structure of luminal domain C of human Niemann-Pick C1 protein.

Odongo, L., Zadrozny, K.K., Diehl, W.E., Luban, J., White, J.M., Ganser-Pornillos, B.K., Tamm, L.K., Pornillos, O.

(2023) Acta Crystallogr F Struct Biol Commun 79: 45-50

• PubMed: 36748341 
• DOI: https://doi.org/10.1107/S2053230X23000705
• Primary Citation Related Structures: 
  8EUS


• PubMed Abstract: 
  

  Niemann-Pick C1 protein (NPC1) is a membrane protein that primarily resides in late endosomes and lysosomes, and plays an important role in cholesterol homeostasis in the cell. The second luminal domain of NPC1 (NPC1-C) serves as the intracellular receptor for Ebola and Marburg viruses. Here, the recombinant production of nonglycosylated and glycosylated NPC1-C and a new crystal form of the nonglycosylated protein are reported. The crystals belonged to space group P2 ₁ and diffracted to 2.3 Å resolution. The structure is similar to other reported structures of NPC1-C, with differences observed in the protruding loops when compared with NPC1-C in complex with Ebola virus glycoprotein or NPC2.

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Organizational Affiliation: 
• Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908, USA.
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.33 kDa 
• Atom Count: 3,503 
• Modeled Residue Count: 414 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPC intracellular cholesterol transporter 1	A [auth C], B [auth A]	262	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.145	α = 90
b = 65.207	β = 91.69
c = 68.534	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Odongo, L., Pornillos, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI30557

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary