Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.44 kDa 
• Atom Count: 5068 
• Modelled Residue Count: 573 
• Deposited Residue Count: 593 
• Unique protein chains: 1

4R12

Crystal structure of the gamma-secretase component Nicastrin

• DOI: 10.2210/pdb4R12/pdb

• Classification: PROTEIN BINDING
• Organism(s): Dictyostelium purpureum
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-08-03 Released: 2014-09-17 
• Deposition Author(s): Xie, T., Yan, C., Zhou, R., Zhao, Y., Sun, L., Yang, G., Lu, P., Ma, D., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.205 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Crystal structure of the gamma-secretase component nicastrin

Xie, T., Yan, C., Zhou, R., Zhao, Y., Sun, L., Yang, G., Lu, P., Ma, D., Shi, Y.

(2014) Proc Natl Acad Sci U S A 

• PubMed: 25197054 
• DOI: 10.1073/pnas.1414837111
• Primary Citation of Related Structures:  
  4R12


• PubMed Abstract: 
  

γ-Secretase is an intramembrane protease responsible for the generation of amyloid-β (Aβ) peptides. Aberrant accumulation of Aβ leads to the formation of amyloid plaques in the brain of patients with Alzheimer's disease. Nicastrin is the putative substrate-recruiting component of the γ-secretase complex. No atomic-resolution structure had been identified on γ-secretase or any of its four components, hindering mechanistic understanding of γ-secretase function. Here we report the crystal structure of nicastrin from Dictyostelium purpureum at 1.95-Å resolution. The extracellular domain of nicastrin contains a large lobe and a small lobe. The large lobe of nicastrin, thought to be responsible for substrate recognition, associates with the small lobe through a hydrophobic pivot at the center. The putative substrate-binding pocket is shielded from the small lobe by a lid, which blocks substrate entry. These structural features suggest a working model of nicastrin function. Analysis of nicastrin structure provides insights into the assembly and architecture of the γ-secretase complex.

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Organizational Affiliation: 

Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	593	Dictyostelium purpureum	Mutation(s): 0  Gene Names: DICPUDRAFT_96800, ncstn
UniProt
Find proteins for F0ZBA6 (Dictyostelium purpureum) Explore F0ZBA6  Go to UniProtKB:  F0ZBA6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.205 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.584	α = 90
b = 65.584	β = 90
c = 344.475	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2014-08-03 
• Released Date: 2014-09-17 
Deposition Author(s): Xie, T., Yan, C., Zhou, R., Zhao, Y., Sun, L., Yang, G., Lu, P., Ma, D., Shi, Y.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary