3T4M | pdb_00003t4m

Ac-AChBP ligand binding domain mutated to human alpha-7 nAChR (intermediate)

PDB DOI: https://doi.org/10.2210/pdb3T4M/pdb

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

Deposited: 2011-07-26 Released: 2011-10-26
Deposition Author(s): Nemecz, A., Taylor, P.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.240 (Depositor), 0.248 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.191 (Depositor)

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

Ligand Structure Quality Assessment

This is version 1.5 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: 265.35 kDa
Atom Count: 17,570
Modeled Residue Count: 2,143
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): 12 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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain V [auth F] MOL2 format, chain V [auth F] mmCIF format, chain V [auth F]	V [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain V [auth F] Interactions & Density Focus chain V [auth F]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Y [auth G] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth G] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth G]	N [auth B], Y [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain N [auth B] Focus chain Y [auth G] Interactions & Density Focus chain N [auth B] Focus chain Y [auth G]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain CA [auth H] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] SDF format, chain DA [auth I] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] MOL2 format, chain DA [auth I] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G] mmCIF format, chain DA [auth I]	BA [auth H] CA [auth H] DA [auth I] L [auth A] O [auth B] BA [auth H], CA [auth H], DA [auth I], L [auth A], O [auth B], R [auth D], T [auth E], W [auth F], Z [auth G]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain Z [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain EA [auth J] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain X [auth G] SDF format, chain Q [auth D] SDF format, chain K [auth A] MOL2 format, chain AA [auth H] MOL2 format, chain EA [auth J] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Q [auth D] MOL2 format, chain K [auth A] mmCIF format, chain AA [auth H] mmCIF format, chain EA [auth J] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Q [auth D] mmCIF format, chain K [auth A]	AA [auth H] EA [auth J] K [auth A] M [auth B] P [auth C] AA [auth H], EA [auth J], K [auth A], M [auth B], P [auth C], Q [auth D], S [auth E], U [auth F], X [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain EA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain EA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain X [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.240 (Depositor), 0.248 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.922	α = 90
b = 152.22	β = 90
c = 176.775	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: 2013-07-17
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.5: 2024-11-20
Changes: Structure summary