Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 181.77 kDa 
• Atom Count: 10,429 
• Modelled Residue Count: 1,332 
• Deposited Residue Count: 1,626 
• Unique protein chains: 6

 6QNO

Rhodopsin-Gi protein complex

• PDB DOI: 10.2210/pdb6QNO/pdb
• EM Map EMD-4598: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Bos taurus, Mus musculus
• Expression System: Escherichia coli BL21, hybrid, Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2019-02-11 Released: 2019-07-10 
• Deposition Author(s): Tsai, C.-J., Marino, J., Adaixo, R.J., Pamula, F., Muehle, J., Maeda, S., Flock, T., Taylor, N.M.I., Mohammed, I., Matile, H., Dawson, R.J.P., Deupi, X., Stahlberg, H., Schertler, G.F.X.
• Funding Organization(s): Swiss National Science Foundation, Swiss Nanoscience Institute

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the rhodopsin-G alpha i-beta gamma complex reveals binding of the rhodopsin C-terminal tail to the G beta subunit.

Tsai, C.J., Marino, J., Adaixo, R., Pamula, F., Muehle, J., Maeda, S., Flock, T., Taylor, N.M., Mohammed, I., Matile, H., Dawson, R.J., Deupi, X., Stahlberg, H., Schertler, G.

(2019) Elife 8

• PubMed: 31251171 
• DOI: 10.7554/eLife.46041
• Primary Citation of Related Structures:  
  6QNK, 6QNO


• PubMed Abstract: 
  

One of the largest membrane protein families in eukaryotes are G protein-coupled receptors (GPCRs). GPCRs modulate cell physiology by activating diverse intracellular transducers, prominently heterotrimeric G proteins. The recent surge in structural data has expanded our understanding of GPCR-mediated signal transduction. However, many aspects, including the existence of transient interactions, remain elusive. We present the cryo-EM structure of the light-sensitive GPCR rhodopsin in complex with heterotrimeric Gi. Our density map reveals the receptor C-terminal tail bound to the Gβ subunit of the G protein, providing a structural foundation for the role of the C-terminal tail in GPCR signaling, and of Gβ as scaffold for recruiting Gα subunits and G protein-receptor kinases. By comparing available complexes, we found a small set of common anchoring points that are G protein-subtype specific. Taken together, our structure and analysis provide new structural basis for the molecular events of the GPCR signaling pathway.

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Organizational Affiliation: 

Department of Biology, ETH Zurich, Zürich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	376	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	340	Bos taurus	Mutation(s): 0  Gene Names: GNB1
UniProt
Find proteins for P62871 (Bos taurus) Explore P62871  Go to UniProtKB:  P62871

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(T) subunit gamma-T1	C [auth G]	74	Bos taurus	Mutation(s): 0  Gene Names: GNGT1 Membrane Entity: Yes
UniProt
Find proteins for P02698 (Bos taurus) Explore P02698  Go to UniProtKB:  P02698

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody fragment light chain	D [auth L]	239	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody fragment heavy chain	E [auth H]	249	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	F [auth R]	348	Bos taurus	Mutation(s): 3  Gene Names: RHO Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699  Go to UniProtKB:  P02699

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET (Subject of Investigation/LOI)	H [auth R]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13-2998
MODEL REFINEMENT	Coot	0.8.9

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Tsai, C.-J., Marino, J., Adaixo, R.J., Pamula, F., Muehle, J., Maeda, S., Flock, T., Taylor, N.M.I., Mohammed, I., Matile, H., Dawson, R.J.P., Deupi, X., Stahlberg, H., Schertler, G.F.X.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_153145
Swiss National Science Foundation	Switzerland	310030B_173335
Swiss National Science Foundation	Switzerland	160805
Swiss Nanoscience Institute	Switzerland	A13.12 NanoGhip
Swiss National Science Foundation	Switzerland	NCCR TransCure

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary