4UM3

Engineered Ls-AChBP with alpha4-alpha4 binding pocket in complex with NS3920


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Achbp Engineered to Mimic the Alpha4-Alpha4 Binding Pocket in Alpha4Beta2 Nicotinic Acetylcholine Receptors Reveals Interface Specific Interactions Important for Binding and Activity

Shahsavar, A.Ahring, P.K.Olsen, J.A.Krintel, C.Kastrup, J.S.Balle, T.Gajhede, M.

(2015) Mol Pharmacol 88: 697

  • DOI: 10.1124/mol.115.098061
  • Primary Citation of Related Structures:  
    4UM1, 4UM3

  • PubMed Abstract: 
  • Neuronal α4β2 nicotinic acetylcholine receptors are attractive drug targets for psychiatric and neurodegenerative disorders and smoking cessation aids. Recently, a third agonist binding site between two α4 subunits in the (α4)(3)(β2)(2) receptor subpopulation was discovered ...

    Neuronal α4β2 nicotinic acetylcholine receptors are attractive drug targets for psychiatric and neurodegenerative disorders and smoking cessation aids. Recently, a third agonist binding site between two α4 subunits in the (α4)(3)(β2)(2) receptor subpopulation was discovered. In particular, three residues, H142, Q150, and T152, were demonstrated to be involved in the distinct pharmacology of the α4-α4 versus α4-β2 binding sites. To obtain insight into the three-dimensional structure of the α4-α4 binding site, a surrogate protein reproducing α4-α4 binding characteristics was constructed by introduction of three point mutations, R104H, L112Q, and M114T, into the binding pocket of Lymnaea stagnalis acetylcholine-binding protein (Ls-AChBP). Cocrystallization with two agonists possessing distinct pharmacologic profiles, NS3920 [1-(6-bromopyridin-3-yl)-1,4-diazepane] and NS3573 [1-(5-ethoxypyridin-3-yl)-1,4-diazepane], highlights the roles of the three residues in determining binding affinities and functional properties of ligands at the α4-α4 interface. Confirmed by mutational studies, our structures suggest a unique ligand-specific role of residue H142 on the α4 subunit. In the cocrystal structure of the mutated Ls-AChBP with the high-efficacy ligand NS3920, the corresponding histidine forms an intersubunit bridge that reinforces the ligand-mediated interactions between subunits. The structures further reveal that the binding site residues gain different and ligand-dependent interactions that could not be predicted based on wild-type Ls-AChBP structures in complex with the same agonists. The results show that an unprecedented correlation between binding in engineered AChBPs and functional receptors can be obtained and provide new opportunities for structure-based design of drugs targeting specific nicotinic acetylcholine receptor interfaces.


    Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark (A.S., J.A.O., C.K., J.S.K., M.G.); Faculty of Pharmacy, University of Sydney, Sydney, New South Wales, Australia (P.K.A., J.A.O., T.B.); Saniona AB, Ballerup, Denmark (P.K.A.); and NeuroSearch A/S, Hellerup, Denmark (J.A.O.) mig@sund.ku.dk thomas.balle@sydney.edu.au.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINE BINDING PROTEIN
A,
B,
C,
D,
E,
229Lymnaea stagnalisMutation(s): 3 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58154
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINE BINDING PROTEINP228Lymnaea stagnalisMutation(s): 3 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58154
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYLCHOLINE BINDING PROTEINS229Lymnaea stagnalisMutation(s): 3 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58154
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
09R
Query on 09R

Download Ideal Coordinates CCD File 
AB [auth L],
AC [auth i],
BB [auth M],
BC [auth j],
CB [auth N],
AB [auth L],
AC [auth i],
BB [auth M],
BC [auth j],
CB [auth N],
CC [auth k],
DB [auth O],
DC [auth l],
EC [auth m],
FB [auth P],
FC [auth n],
GB [auth Q],
HB [auth R],
IB [auth S],
JB [auth T],
KB [auth U],
MB [auth V],
NB [auth W],
OA [auth A],
OB [auth X],
PB [auth Y],
QA [auth B],
QB [auth Z],
RA [auth C],
RB [auth a],
SA [auth D],
SB [auth b],
TA [auth E],
TB [auth c],
UA [auth F],
UB [auth d],
VA [auth G],
WA [auth H],
WB [auth f],
XA [auth I],
XB [auth f],
YA [auth J],
YB [auth g],
ZA [auth K],
ZB [auth h]
1-(6-bromopyridin-3-yl)-1,4-diazepane
C10 H14 Br N3
JRNYLCIPPWHNEJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EB [auth O],
PA [auth A],
VB [auth d]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
LB [auth V]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
09R BindingDB:  4UM3 Ki: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.49α = 90
b = 145.418β = 101.29
c = 234.906γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2015-09-02
    Changes: Database references
  • Version 2.0: 2017-11-15
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary