3SIO | pdb_00003sio

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

PDB DOI: https://doi.org/10.2210/pdb3SIO/pdb

Classification: RECEPTOR
Organism(s): Aplysia californica
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2011-06-19 Released: 2011-10-26
Deposition Author(s): Nemecz, A., Taylor, P.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.230 (Depositor), 0.224 (DCC)
R-Value Work:
0.182 (Depositor), 0.178 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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 Biological Chem 286: 42555-42565

PubMed: 22009746 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M111.286583
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 277.71 kDa
Atom Count: 19,701
Modeled Residue Count: 2,162
Deposited Residue Count: 2,300
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble acetylcholine receptor	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	230	Aplysia californica	Mutation(s): 18 Gene Names: AChBP
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WSF8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, M, O	2		N-Glycosylation	Interactions Focus chain K Focus chain M Focus chain O Interactions & Density Focus chain K Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	7		N-Glycosylation	Interactions Focus chain L Focus chain P Interactions & Density Focus chain L Focus chain P
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	6		N-Glycosylation	Interactions Focus chain N Focus chain Q Interactions & Density Focus chain N Focus chain Q
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLK Query on MLK Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain U [auth B] SDF format, chain S [auth A] SDF format, chain QA [auth J] SDF format, chain NA [auth I] SDF format, chain KA [auth H] SDF format, chain HA [auth G] SDF format, chain FA [auth F] SDF format, chain DA [auth E] SDF format, chain AA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain U [auth B] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth J] MOL2 format, chain NA [auth I] MOL2 format, chain KA [auth H] MOL2 format, chain HA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain U [auth B] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth J] mmCIF format, chain NA [auth I] mmCIF format, chain KA [auth H] mmCIF format, chain HA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain AA [auth D]	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		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain NA [auth I] Focus chain QA [auth J] Focus chain S [auth A] Focus chain U [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain KA [auth H] Focus chain NA [auth I] Focus chain QA [auth J] Focus chain S [auth A] Focus chain U [auth B] Focus chain X [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain R [auth A] SDF format, chain PA [auth J] SDF format, chain LA [auth I] SDF format, chain IA [auth H] SDF format, chain EA [auth F] SDF format, chain CA [auth E] MOL2 format, chain V [auth C] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain LA [auth I] MOL2 format, chain IA [auth H] MOL2 format, chain EA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain V [auth C] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain LA [auth I] mmCIF format, chain IA [auth H] mmCIF format, chain EA [auth F] mmCIF format, chain CA [auth E]	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		Interactions Focus chain CA [auth E] Focus chain EA [auth F] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain PA [auth J] Focus chain R [auth A] Focus chain V [auth C] Interactions & Density Focus chain CA [auth E] Focus chain EA [auth F] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain PA [auth J] Focus chain R [auth A] Focus chain V [auth C]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain OA [auth I] SDF format, chain JA [auth H] SDF format, chain GA [auth G] SDF format, chain BA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain OA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain BA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain OA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain BA [auth D]	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		Interactions Focus chain BA [auth D] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain OA [auth I] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain OA [auth I] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain MA [auth I] SDF format, chain Y [auth C] MOL2 format, chain MA [auth I] MOL2 format, chain Y [auth C] mmCIF format, chain MA [auth I] mmCIF format, chain Y [auth C]	MA [auth I], Y [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain MA [auth I] Focus chain Y [auth C] Interactions & Density Focus chain MA [auth I] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.230 (Depositor), 0.224 (DCC)
R-Value Work: 0.182 (Depositor), 0.178 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.218	α = 90
b = 142.366	β = 90.02
c = 144.477	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Nemecz, A.

Taylor, P.W.

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