6FUF

Crystal structure of the rhodopsin-mini-Go complex

• PDB DOI: https://doi.org/10.2210/pdb6FUF/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2018-02-27 Released: 2018-10-03 
• Deposition Author(s): Tsai, C.-J., Weinert, T., Muehle, J., Pamula, F., Nehme, R., Flock, T., Nogly, P., Edwards, P.C., Carpenter, B., Gruhl, T., Ma, P., Deupi, X., Standfuss, J., Tate, C.G., Schertler, G.F.X.
• Funding Organization(s): Swiss National Science Foundation, European Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 0.280 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 60.62 kDa 
• Atom Count: 4,008 
• Modelled Residue Count: 497 
• Deposited Residue Count: 530 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	316	Bos taurus	Mutation(s): 3  Gene Names: RHO Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(o) subunit alpha	B	214	Homo sapiens	Mutation(s): 8  Gene Names: GNAO1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P09471 (Homo sapiens) Explore P09471  Go to UniProtKB:  P09471
PHAROS:  P09471 GTEx:  ENSG00000087258

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	C [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 0.280 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.359	α = 90
b = 151.359	β = 90
c = 96.652	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Tsai, C.-J., Weinert, T., Muehle, J., Pamula, F., Nehme, R., Flock, T., Nogly, P., Edwards, P.C., Carpenter, B., Gruhl, T., Ma, P., Deupi, X., Standfuss, J., Tate, C.G., Schertler, G.F.X.

---

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_153145
Swiss National Science Foundation	Switzerland	310030B_173335
Swiss National Science Foundation	Switzerland	310030B_173335
Swiss National Science Foundation	Switzerland	31003A_159558
European Research Council	United Kingdom	EMPSI, 339995

Revision History  

• Version 1.0: 2018-10-03
  Type: Initial release
  
• Version 1.1: 2018-10-10
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary