Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 42.02 kDa 
• Atom Count: 2830 
• Residue Count: 327 
• Unique protein chains: 1

6FKD

Crystal structure of N2C/D282C stabilized opsin bound to RS16

• DOI: 10.2210/pdb6FKD/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Bos taurus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2018-01-23 Released: 2018-04-04 
• Deposition Author(s): Mattle, D., Standfuss, J., Dawson, R.
• Funding Organization(s): Roche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.250 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Literature

Ligand channel in pharmacologically stabilized rhodopsin.

Mattle, D., Kuhn, B., Aebi, J., Bedoucha, M., Kekilli, D., Grozinger, N., Alker, A., Rudolph, M.G., Schmid, G., Schertler, G.F.X., Hennig, M., Standfuss, J., Dawson, R.J.P.

(2018) Proc Natl Acad Sci U S A 115: 3640-3645

• PubMed: 29555765 
• DOI: 10.1073/pnas.1718084115
• Primary Citation of Related Structures:  
  6FK6, 6FK8, 6FK7, 6FK9, 6FKD, 6FKC, 6FKB, 6FKA


• PubMed Abstract: 
  

In the degenerative eye disease retinitis pigmentosa (RP), protein misfolding leads to fatal consequences for cell metabolism and rod and cone cell survival. To stop disease progression, a therapeutic approach focuses on stabilizing inherited protein mutants of the G protein-coupled receptor (GPCR) rhodopsin using pharmacological chaperones (PC) that improve receptor folding and trafficking. In this study, we discovered stabilizing nonretinal small molecules by virtual and thermofluor screening and determined the crystal structure of pharmacologically stabilized opsin at 2.4 Å resolution using one of the stabilizing hits (S-RS1). Chemical modification of S-RS1 and further structural analysis revealed the core binding motif of this class of rhodopsin stabilizers bound at the orthosteric binding site. Furthermore, previously unobserved conformational changes are visible at the intradiscal side of the seven-transmembrane helix bundle. A hallmark of this conformation is an open channel connecting the ligand binding site with the membrane and the intradiscal lumen of rod outer segments. Sufficient in size, the passage permits the exchange of hydrophobic ligands such as retinal. The results broaden our understanding of rhodopsin's conformational flexibility and enable therapeutic drug intervention against rhodopsin-related retinitis pigmentosa.

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Organizational Affiliation: 

Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	349	Bos taurus	Mutation(s): 1  Gene Names: RHO
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  G Protein-Coupled Receptors (GPCRs): Class A	Protein:  Rhodopsin, N2C/D282C stabilized opsin bound to RS01
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DL2	A	5-chloranyl-2-(2-oxidanylidene-2-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-ethyl)-3~{H}-pyridin-6-one C18 H17 Cl N2 O4 PBLFEEIOVIDZSW-UHFFFAOYSA-N
BOG	A	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PLM	A	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.250 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 243.431	α = 90
b = 243.431	β = 90
c = 111.782	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-23 
• Released Date: 2018-04-04 
Deposition Author(s): Mattle, D., Standfuss, J., Dawson, R.

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Funding Organization	Location	Grant Number
Roche	Switzerland	RPF

Revision History 

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary