3SIO

Ac-AChBP ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7 nAChR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Creating an alpha-7 nicotinic acetylcholine recognition domain from the acetylcholine binding protein: crystallographic and ligand selectivity analyses

Nemecz, A.Taylor, P.

(2011) J Biol Chem 286: 42555-42565

  • DOI: https://doi.org/10.1074/jbc.M111.286583
  • Primary Citation of Related Structures:  
    3SH1, 3SIO, 3T4M

  • PubMed Abstract: 

    Determining the structure of the ligand-binding domain of the nicotinic acetylcholine receptor (nAChR) has been a long standing goal in the design of selective drugs useful in implicated diseases for this prevalent receptor family. Acetylcholine-binding proteins have proven to be valuable surrogates with structural similarity and sequence identity to the extracellular domain of the nicotinic receptor, yet these soluble proteins have their unique features and do not serve as exact replicates of the nAChRs of interest. Here we systematically modify the sequence of these proteins toward the homomeric human α7 nAChR. These chimeric proteins exhibit a shift in affinities to reflect α7 binding characteristics yet maintain expression levels and stability conducive for crystallization. We also present a pentameric humanoid nAChR extracellular domain with the structural determination of the α7 nAChR glycosylation site.


  • Organizational Affiliation

    Departments of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0650; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0650.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble acetylcholine receptor
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
230Aplysia californicaMutation(s): 18 
Gene Names: AChBP
UniProt
Find proteins for Q8WSF8 (Aplysia californica)
Explore Q8WSF8 
Go to UniProtKB:  Q8WSF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WSF8
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, M, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
L, P
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N, Q
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLK
Query on MLK

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
FA [auth F]
HA [auth G]
KA [auth H]
AA [auth D],
DA [auth E],
FA [auth F],
HA [auth G],
KA [auth H],
NA [auth I],
QA [auth J],
S [auth A],
U [auth B],
X [auth C]
METHYLLYCACONITINE
C37 H50 N2 O10
XLTANAWLDBYGFU-VTLKBQQISA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth E]
EA [auth F]
IA [auth H]
LA [auth I]
PA [auth J]
CA [auth E],
EA [auth F],
IA [auth H],
LA [auth I],
PA [auth J],
R [auth A],
V [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
MA [auth I],
Y [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
BA [auth D]
GA [auth G]
JA [auth H]
OA [auth I]
T [auth B]
BA [auth D],
GA [auth G],
JA [auth H],
OA [auth I],
T [auth B],
W [auth C],
Z [auth D]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MLK PDBBind:  3SIO Ki: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.218α = 90
b = 142.366β = 90.02
c = 144.477γ = 90
Software Package:
Software NamePurpose
CCP4model building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2024-04-03
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary