Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 7

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Loop B is a major structural component of the 5-HT3 receptor.

(2008) Biophys J 95

PubMed: 18931259 | PubMedCentral: PMC2599823 | DOI: 10.1529/biophysj.108.135624

Three-dimensional models of the extracellular region of the 5-HT 3 receptor were built using MODELER 6v2 ( 22 ) based on the crystal structure of AChBP in different states; unbound (Protein Data Bank ... PDB) ID 2byn), agonist bound (carbomylcholine, PDB ID 1uv6 and epibatidine, PDB ID 2byq) and antagonist bound (2-methyllcaconitine, PDB ID 2byr and α -cobratoxin, PDB ID 1yi5).

( C ) Agonist bound, (modeled from AChBP with epibatidine, PDB ID 2byq).

Publication Year: 2008


A structural and mutagenic blueprint for molecular recognition of strychnine and d-tubocurarine by different cys-loop receptors.

(2011) PLoS Biol 9

PubMed: 21468359 | PubMedCentral: PMC3066128 | DOI: 10.1371/journal.pbio.1001034

Accession Numbers Protein Data Bank accession codes for previously published X-ray crystal structures are: Ac-AChBP in complex with lobeline (2bys), epibatidine (2byq), imidacloprid (3c79), thiaclopri... (3c84), HEPES (2br7), polyethyleneglycol (2byn), DMXBA (2wnj), 4OH-DMXBA (2wn9), cocaine (2pgz), anabaseine (2wnl), in silico compound 31 (2w8f), MLA (2byr), in silico compound 35 (2w8g), sulfates (3gua), α-conotoxin ImI (2c9t and 2byp), α-conotoxin PnIA variant (2br8), α-conotoxin TxIA (2uz6), apo state (2w8e), Y53C-MMTS (2xz5) with acetylcholine, Y53C-MTSET (2xz6).

Publication Year: 2011


Identification of a negative allosteric site on human ?4?2 and ?3?4 neuronal nicotinic acetylcholine receptors.

(2011) PLoS One 6

PubMed: 21949802 | PubMedCentral: PMC3174232 | DOI: 10.1371/journal.pone.0024949

Antagonist Docking to Ternary Complex After the initial round of blind docking to the unbound nAChR models, the epibatidine docking with the smallest RMSD from the AChBP binding mode (as found in PDB ... D: 2BYQ) was kept as part of each nAChR structure.

Publication Year: 2011


An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors.

(2012) J Gen Physiol 140

PubMed: 22732309 | PubMedCentral: PMC3382718 | DOI: 10.1085/jgp.201210801

: 2WN9 , 2WNL , 2BYN (apo-), 2PGZ , 2W8F , 2W8G , 2XYT , 2WNJ , 2BYQ , 2BR7 , 3C79 , 2BYR , 2XYS , 3GUA , 3C84 , 2WNC , 2XZ6 , 2XZ5 , and 2BYS .

Publication Year: 2012


A unified model of the GABA(A) receptor comprising agonist and benzodiazepine binding sites.

(2013) PLoS One 8

PubMed: 23308109 | PubMedCentral: PMC3538749 | DOI: 10.1371/journal.pone.0052323

We identified a hydrophobic-X-hydrophobic motif (corresponding to V V V in the GABA A R α 1 -subunit), forming a short β-strand of three residues in GluCl, ELIC, the bacterial ion chan... el GLIC (PDB ID: 3EAM) the mouse nAChR α 1 -subunit (PDB ID: 2QC1) and in AChBPs from Aplysia californica (PDB ID: 2BYQ) and Bulinus truncatus (PDB ID: 2BJ0) [27] , [34] , [35] , [43] .

Publication Year: 2013


Allosteric activation mechanism of the cys-loop receptors.

(2009) Acta Pharmacol Sin 30

PubMed: 19444220 | PubMedCentral: PMC4002373 | DOI: 10.1038/aps.2009.51

(A) AChBPs crystallized in apo state (red, from 2BYN), Epibatidine (agonist)-bound state (green, from 2BYQ) and ImI (antagonist)-bound state (blue, from 2BYP).

Publication Year: 2009


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4514475

A,B) X-ray crystallographic structures of the chains A and E of AChBP from Aplysia californica (PDB entry: 2BYQ [ 26 ]), and GluCl from Caenorhabditis elegans (PDB entry: 3RIF, [ 41 ]), respectively.

Materials and Methods Homology modeling As templates for homology modeling of the α 7 nAChR we used the following X-ray structures: (i) AChBP from Aplysia californica bound to epibatidine (PDB entry: 2BYQ [ 26 ]), (ii) GluCl from Caenorhabditis elegans (PDB entry: 3RIF [ 41 ]).

The two template structures have been manually handled to build a chimera protein in which the ECD domain (residues 0–203 in the chain A of 2BYQ) except the Cys-loop (residues 127–140 in the chain A of 2BYQ) was taken from AChBP, and the TMD domain (residues 209–339 in the chain A of 3RIF) as well as the Cys-loop (residues 130–144 in the chain A of 3RIF) were taken from GluCl.

As for the quality of the template, we used crystallographic structures with the highest resolution available (2BYQ: 3.4 Å and 3RIF: 3.35 Å), as described in Materials and Methods.

The residues of the superimposed structures are: (i) 55–62, 77–80, 107–118, 91–93, 138–147 for 2BYQ, and (ii) 54–61, 76–79, 110–121, 91–93, 141–150 for 3RIF.

C) Superimposed subunits from 2BYQ (green) and 3RIF (in blue) using the residues defined above.

Publication Year: 2015