6CRK

Heterotrimeric G-protein in complex with an antibody fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Development of an antibody fragment that stabilizes GPCR/G-protein complexes.

Maeda, S.Koehl, A.Matile, H.Hu, H.Hilger, D.Schertler, G.F.X.Manglik, A.Skiniotis, G.Dawson, R.J.P.Kobilka, B.K.

(2018) Nat Commun 9: 3712-3712

  • DOI: 10.1038/s41467-018-06002-w

  • PubMed Abstract: 
  • Single-particle cryo-electron microscopy (cryo-EM) has recently enabled high-resolution structure determination of numerous biological macromolecular complexes. Despite this progress, the application of high-resolution cryo-EM to G protein coupled re ...

    Single-particle cryo-electron microscopy (cryo-EM) has recently enabled high-resolution structure determination of numerous biological macromolecular complexes. Despite this progress, the application of high-resolution cryo-EM to G protein coupled receptors (GPCRs) in complex with heterotrimeric G proteins remains challenging, owning to both the relative small size and the limited stability of these assemblies. Here we describe the development of antibody fragments that bind and stabilize GPCR-G protein complexes for the application of high-resolution cryo-EM. One antibody in particular, mAb16, stabilizes GPCR/G-protein complexes by recognizing an interface between Gα and Gβγ subunits in the heterotrimer, and confers resistance to GTPγS-triggered dissociation. The unique recognition mode of this antibody makes it possible to transfer its binding and stabilizing effect to other G-protein subtypes through minimal protein engineering. This antibody fragment is thus a broadly applicable tool for structural studies of GPCR/G-protein complexes.


    Organizational Affiliation

    Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.,Laboratory of Biomolecular Research, Paul Scherrer Institute, 5232, Villigen, Switzerland.,Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94143, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA. kobilka@stanford.edu.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA.,Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland. roger.dawson@roche.com.,Department of Anesthesia and Perioperative Care, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94143, USA.,Department of Structural Biology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1
A
355Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Find proteins for P63096 (Homo sapiens)
Go to Gene View: GNAI1
Go to UniProtKB:  P63096
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
B
345Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Go to Gene View: GNB1
Go to UniProtKB:  P62873
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
G
71Homo sapiensMutation(s): 1 
Gene Names: GNG2
Find proteins for P59768 (Homo sapiens)
Go to Gene View: GNG2
Go to UniProtKB:  P59768
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
single-chain Fv
H
259N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 58.514α = 90.00
b = 104.739β = 90.00
c = 211.821γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release