6QNO

Rhodopsin-Gi protein complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Division of Biology and Chemistry / Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1376Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1340Bos taurusMutation(s): 0 
UniProt
Find proteins for P62871 (Bos taurus)
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Go to UniProtKB:  P62871
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UniProt GroupP62871
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(T) subunit gamma-T1C [auth G]74Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02698 (Bos taurus)
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UniProt GroupP02698
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab antibody fragment light chainD [auth L]239Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Fab antibody fragment heavy chainE [auth H]249Mus musculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RhodopsinF [auth R]348Bos taurusMutation(s): 3 
Gene Names: RHO
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
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UniProt GroupP02699
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Oligosaccharides

Help

Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
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:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.13-2998
MODEL REFINEMENTCoot0.8.9

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_153145
Swiss National Science FoundationSwitzerland310030B_173335
Swiss National Science FoundationSwitzerland160805
Swiss Nanoscience InstituteSwitzerlandA13.12 NanoGhip
Swiss National Science FoundationSwitzerlandNCCR TransCure

Revision History  (Full details and data files)

  • 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