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 6QNK | pdb_00006qnk

Antibody FAB fragment targeting Gi protein heterotrimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6QNK

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 112.81 kDa 
  • Atom Count: 7,313 
  • Modeled Residue Count: 876 
  • Deposited Residue Count: 1,022 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB light chain
A, C
239Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB heavy chain
B, D
272Mus musculusMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
R [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
K [auth A],
Y [auth D]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
MLT

Query on MLT



Download:Ideal Coordinates CCD File
P [auth B],
Q [auth B],
U [auth C],
V [auth C]
D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.94α = 90
b = 68.08β = 127.2
c = 133.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_153145
Swiss National Science FoundationSwitzerland310030B_173335
Swiss National Science FoundationSwitzerland160805
SwitzerlandSwiss Nanoscience Institute A13.12 NanoGhip

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary