5FPP

Structure of a pre-reaction ternary complex between sarin- acetylcholinesterase and HI-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of a Prereaction Complex between the Nerve Agent Sarin, its Biological Target Acetylcholinesterase, and the Antidote Hi-6.

Allgardsson, A.Berg, L.Akfur, C.Hornberg, A.Worek, F.Linusson, A.Ekstrom, F.J.

(2016) Proc Natl Acad Sci U S A 113: 5514

  • DOI: 10.1073/pnas.1523362113
  • Primary Citation of Related Structures:  
    5FPP, 5FPQ

  • PubMed Abstract: 
  • Organophosphorus nerve agents interfere with cholinergic signaling by covalently binding to the active site of the enzyme acetylcholinesterase (AChE). This inhibition causes an accumulation of the neurotransmitter acetylcholine, potentially leading to overstimulation of the nervous system and death ...

    Organophosphorus nerve agents interfere with cholinergic signaling by covalently binding to the active site of the enzyme acetylcholinesterase (AChE). This inhibition causes an accumulation of the neurotransmitter acetylcholine, potentially leading to overstimulation of the nervous system and death. Current treatments include the use of antidotes that promote the release of functional AChE by an unknown reactivation mechanism. We have used diffusion trap cryocrystallography and density functional theory (DFT) calculations to determine and analyze prereaction conformers of the nerve agent antidote HI-6 in complex with Mus musculus AChE covalently inhibited by the nerve agent sarin. These analyses reveal previously unknown conformations of the system and suggest that the cleavage of the covalent enzyme-sarin bond is preceded by a conformational change in the sarin adduct itself. Together with data from the reactivation kinetics, this alternate conformation suggests a key interaction between Glu202 and the O-isopropyl moiety of sarin. Moreover, solvent kinetic isotope effect experiments using deuterium oxide reveal that the reactivation mechanism features an isotope-sensitive step. These findings provide insights into the reactivation mechanism and provide a starting point for the development of improved antidotes. The work also illustrates how DFT calculations can guide the interpretation, analysis, and validation of crystallographic data for challenging reactive systems with complex conformational dynamics.


    Organizational Affiliation

    Department of CBRN Defence and Security, Swedish Defence Research Agency, SE-90182 Umea, Sweden; anna.linusson@umu.se freeks@foi.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASEA, B548Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus)
Explore P21836 
Go to UniProtKB:  P21836
IMPC:  MGI:87876
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HI6
Query on HI6

Download Ideal Coordinates CCD File 
G [auth A], H [auth B]4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM
C14 H16 N4 O3
FJZDLOMCEPUCII-UHFFFAOYSA-P
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
E [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
AE3
Query on AE3

Download Ideal Coordinates CCD File 
F [auth A], I [auth B]2-(2-ETHOXYETHOXY)ETHANOL
C6 H14 O3
XXJWXESWEXIICW-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download Ideal Coordinates CCD File 
D [auth A], J [auth B]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SGB
Query on SGB
A, BL-PEPTIDE LINKINGC7 H16 N O5 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HI6Kd:  234000   nM  BindingDB
HI6Kd:  15000   nM  BindingDB
HI6IC50:  667800   nM  BindingDB
HI6IC50:  1360000   nM  BindingDB
HI6Kd:  27000   nM  BindingDB
HI6Kd:  100000   nM  Binding MOAD
HI6Kd:  93000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.825α = 90
b = 111.552β = 90
c = 227.556γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2021-05-12
    Changes: Derived calculations, Structure summary