Glycine receptor mechanism elucidated by electron cryo-microscopy.

Du, J; Lu, W; Wu, S; Cheng, Y; Gouaux, E.

Macromolecule Content

Unique protein chains: 1

3JAD

Structure of alpha-1 glycine receptor by single particle electron cryo-microscopy, strychnine-bound state

DOI: 10.2210/pdb3jad/pdb
EMDataBank: EMD-6344

Classification: SIGNALING PROTEIN / ANTAGONIST
Deposited: 2015-06-08 Released: 2015-09-09
Deposition author(s): Du, J., Lu, W., Wu, S.P., Cheng, Y.F., Gouaux, E.
Organism: Danio rerio
Expression System: Spodoptera frugiperda

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.9 Å
Reconstruction Method: Single Particle

wwPDB Validation 3D Report Full Report

Literature

Macromolecules

Classification: SIGNALING PROTEIN / ANTAGONIST

Total Structure Weight: 199913.67

Macromolecule Entities
Molecule	Chains	Length	Organism	Details
Glycine receptor subunit alphaZ1	A, B, C, D, E	342	Danio rerio	Gene Name(s): glra1
Metabolic Pathways Maps: Reactions: ESCHER BiGG
Protein Feature View - UniProtKB AC: O93430 UniProt Full Protein Feature View for O93430 Find similar proteins by: Sequence \| Structure Show Detailed Protein Feature View for O93430/3JAD

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Cys-Loop Receptor Family

Protein Name: α1 GlyR Glycine receptor in complex with strychnine

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
SY9 Query on SY9 Download SDF File Download CCD File	A, B, C, D, E	STRYCHNINE C₂₁ H₂₂ N₂ O₂ QMGVPVSNSZLJIA-FVWCLLPLSA-N	Poseview Image of SY9 in 3JAD Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)
NAG Query on NAG Download SDF File Download CCD File	A, B, C, D, E	N-ACETYL-D-GLUCOSAMINE C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N	Poseview Image of NAG in 3JAD Help Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions. Source Information Interactions are determined by geometric criteria as described in K. Stierand, M. Rarey (2010), Drawing the PDB: Protein-ligand complexes in two dimensions, ACS Med. Chem. Lett., DOI: 10.1021/ml100164p. Ions and some metal complexes are excluded, as well as cases where no interaction profile could be generated. Poseview diagrams can be calculated for approximately 92% of the remaining complexes in the PDB. PoseView is developed at the Center for Bioinformatics Hamburg and jointly provided with BioSolveIT as a community service at the PDB. A stand-alone version is provided by BioSolveIT.	Ligand Explorer NGL Binding Pocket (JSmol) Electron Density (JSmol)