5VDH | pdb_00005vdh

Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607, Glycine, and Ivermectin

• PDB DOI: https://doi.org/10.2210/pdb5VDH/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2017-04-03 Released: 2017-05-24 
• Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Human GlyR alpha 3 Bound to Ivermectin.

Huang, X., Chen, H., Shaffer, P.L.

(2017) Structure 25: 945-950.e2

• PubMed: 28479061 
• DOI: https://doi.org/10.1016/j.str.2017.04.007
• Primary Citation Related Structures: 
  5VDH, 5VDI


• PubMed Abstract: 
  

  Ivermectin acts as a positive allosteric modulator of several Cys-loop receptors including the glutamate-gated chloride channels (GluCls), γ-aminobutyric acid receptors (GABA _A Rs), glycine receptors (GlyRs), and neuronal α7-nicotinic receptors (α7 nAChRs). The crystal structure of Caenorhabditis elegans GluCl complexed with ivermectin revealed the details of its ivermectin binding site. Although the electron microscopy structure of zebrafish GlyRα1 complexed with ivermectin demonstrated a similar binding orientation, detailed structural information on the ivermectin binding and pore opening for Cys-loop receptors in vertebrates has been elusive. Here we present the crystal structures of human GlyRα3 in complex with ivermectin at 2.85 and 3.08 Å resolution. Our structures allow us to explore in detail the molecular recognition of ivermectin by GlyRs, GABA _A Rs, and α7 nAChRs. Comparisons with previous structures reveal how the ivermectin binding expands the ion channel pore. Our results hold promise in structure-based design of GlyR modulators for the treatment of neuropathic pain.

---

Organizational Affiliation: 
• Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA. Electronic address: [e-mail].
Department of Protein Technologies, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA.
Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney Street, Cambridge, MA 02142, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 216.63 kDa 
• Atom Count: 14,064 
• Modeled Residue Count: 1,700 
• Deposited Residue Count: 1,810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-3	A, B, C, D, E	362	Homo sapiens	Mutation(s): 0  Gene Names: GLRA3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O75311 (Homo sapiens) Explore O75311  Go to UniProtKB:  O75311
PHAROS:  O75311 GTEx:  ENSG00000145451
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O75311-1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IVM	H [auth A], M [auth B], Q [auth C], V [auth D], Z [auth E]	(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside C48 H74 O14 AZSNMRSAGSSBNP-XPNPUAGNSA-N
7C6	F [auth A], K [auth B], O [auth C], T [auth D], X [auth E]	(3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one C19 H19 N3 O5 S MXNQASHPCAMJHG-UCMVZMLTSA-N
NAG	S [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLY	G [auth A], L [auth B], P [auth C], U [auth D], Y [auth E]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN	AA [auth E], I [auth A], N [auth B], R [auth C], W [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
7C6	BindingDB:  5VDH	Kd: 11 (nM) from 1 assay(s)
		EC50: min: 16, max: 50 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.236 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.065	α = 90
b = 119.065	β = 90
c = 429.934	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

Revision History  

• Version 1.0: 2017-05-24
  Type: Initial release
  
• Version 1.1: 2017-06-21
  Changes: Database references, Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-23
  Changes: Structure summary