6CRK

Heterotrimeric G-protein in complex with an antibody fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305, USA. kobilka@stanford.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
single-chain FvH259Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1A355Homo sapiensMutation(s): 0 
Gene Names: GNAI1
Find proteins for P63096 (Homo sapiens)
Explore P63096 
Go to UniProtKB:  P63096
NIH Common Fund Data Resources
PHAROS  P63096
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1B345Homo sapiensMutation(s): 0 
Gene Names: GNB1
Find proteins for P62873 (Homo sapiens)
Explore P62873 
Go to UniProtKB:  P62873
NIH Common Fund Data Resources
PHAROS  P62873
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2G71Homo sapiensMutation(s): 1 
Gene Names: GNG2
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
NIH Common Fund Data Resources
PHAROS  P59768
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 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
b = 104.739β = 90
c = 211.821γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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