Macromolecule Content

Total Structure Weight: 1053.02 kDa
Atom Count: 64774
Modelled Residue Count: 7922
Deposited Residue Count: 9159
Unique protein chains: 3

4UM3

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

PDB DOI: 10.2210/pdb4UM3/pdb

Classification: SIGNALING PROTEIN
Organism(s): Lymnaea stagnalis
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2014-05-14 Released: 2015-07-22
Deposition Author(s): Shahsavar, A., Kastrup, J.S., Balle, T., Gajhede, M.

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

PubMed: 26180047 Search on PubMed
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. 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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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINE BINDING PROTEIN	A, B, C, D, E, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, Q, R, T, U, V, W, X, Y, Z, AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n]	229	Lymnaea stagnalis	Mutation(s): 3
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154 Go to UniProtKB: P58154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P58154
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINE BINDING PROTEIN	P	228	Lymnaea stagnalis	Mutation(s): 3
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154 Go to UniProtKB: P58154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P58154
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINE BINDING PROTEIN	S	229	Lymnaea stagnalis	Mutation(s): 3
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154 Go to UniProtKB: P58154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P58154
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
09R Query on 09R Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain AC [auth i] SDF format, chain BB [auth M] SDF format, chain BC [auth j] SDF format, chain CB [auth N] SDF format, chain CC [auth k] SDF format, chain DB [auth O] SDF format, chain DC [auth l] SDF format, chain EC [auth m] SDF format, chain FC [auth n] SDF format, chain GB [auth Q] SDF format, chain HB [auth R] SDF format, chain IB [auth S] SDF format, chain KB [auth U] SDF format, chain MB [auth V] SDF format, chain NB [auth W] SDF format, chain OA [auth A] SDF format, chain OB [auth X] SDF format, chain PB [auth Y] SDF format, chain QA [auth B] SDF format, chain QB [auth Z] SDF format, chain RA [auth C] SDF format, chain RB [auth a] SDF format, chain SA [auth D] SDF format, chain SB [auth b] SDF format, chain TA [auth E] SDF format, chain TB [auth c] SDF format, chain UA [auth F] SDF format, chain UB [auth d] SDF format, chain VA [auth G] SDF format, chain WA [auth H] SDF format, chain WB [auth f] SDF format, chain XA [auth I] SDF format, chain XB [auth f] SDF format, chain YA [auth J] SDF format, chain YB [auth g] SDF format, chain ZA [auth K] SDF format, chain ZB [auth h] SDF format, chain FB [auth P] SDF format, chain JB [auth T] MOL2 format, chain AB [auth L] MOL2 format, chain AC [auth i] MOL2 format, chain BB [auth M] MOL2 format, chain BC [auth j] MOL2 format, chain CB [auth N] MOL2 format, chain CC [auth k] MOL2 format, chain DB [auth O] MOL2 format, chain DC [auth l] MOL2 format, chain EC [auth m] MOL2 format, chain FC [auth n] MOL2 format, chain GB [auth Q] MOL2 format, chain HB [auth R] MOL2 format, chain IB [auth S] MOL2 format, chain KB [auth U] MOL2 format, chain MB [auth V] MOL2 format, chain NB [auth W] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth X] MOL2 format, chain PB [auth Y] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth Z] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth a] MOL2 format, chain SA [auth D] MOL2 format, chain SB [auth b] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth c] MOL2 format, chain UA [auth F] MOL2 format, chain UB [auth d] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth H] MOL2 format, chain WB [auth f] MOL2 format, chain XA [auth I] MOL2 format, chain XB [auth f] MOL2 format, chain YA [auth J] MOL2 format, chain YB [auth g] MOL2 format, chain ZA [auth K] MOL2 format, chain ZB [auth h] MOL2 format, chain FB [auth P] MOL2 format, chain JB [auth T]	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 SDF format, chain EB [auth O] SDF format, chain PA [auth A] SDF format, chain VB [auth d] MOL2 format, chain EB [auth O] MOL2 format, chain PA [auth A] MOL2 format, chain VB [auth d]	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 SDF format, chain LB [auth V] MOL2 format, chain LB [auth V]	LB [auth V]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding 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 = 135.49	α = 90
b = 145.418	β = 101.29
c = 234.906	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-05-14
Released Date: 2015-07-22

Deposition Author(s):

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