5LV0 | pdb_00005lv0

Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product

• PDB DOI: https://doi.org/10.2210/pdb5LV0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-09-12 Released: 2017-12-06 
• Deposition Author(s): Masuyer, G., Berntsson, R.P.-A., Teixeira, P.F., Kmiec, B., Glaser, E., Stenmark, P.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structural and functional analysis of Neurolysin, a new component of the mitochondrial peptidolytic network

Teixeira, P.F., Masuyer, G., Pinho, C., Branca, R.M.M., Kmiec, B., Wallin, C., Warmlander, S., Berntsson, R.P.-A., Ankarcrona, M., Graslund, A., Lehtio, J., Stenmark, P., Glaser, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 158.61 kDa 
• Atom Count: 10,786 
• Modeled Residue Count: 1,335 
• Deposited Residue Count: 1,384 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurolysin, mitochondrial	A, B	686	Homo sapiens	Mutation(s): 1  Gene Names: NLN, AGTBP, KIAA1226 EC: 3.4.24.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYT8 (Homo sapiens) Explore Q9BYT8  Go to UniProtKB:  Q9BYT8
PHAROS:  Q9BYT8 GTEx:  ENSG00000123213

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-VAL-VAL amyloid 35-40 fragment	C, D	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens) Explore P05067  Go to UniProtKB:  P05067
PHAROS:  P05067 GTEx:  ENSG00000142192

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.341	α = 90
b = 131.341	β = 90
c = 195.979	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Masuyer, G., Berntsson, R.P.-A., Teixeira, P.F., Kmiec, B., Glaser, E., Stenmark, P.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2014-5667

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description