3JBQ | pdb_00003jbq

Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history

Literature

Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6.

Zhang, Z.He, F.Constantine, R.Baker, M.L.Baehr, W.Schmid, M.F.Wensel, T.G.Agosto, M.A.

(2015) J Biological Chem 290: 12833-12843

  • DOI: https://doi.org/10.1074/jbc.M115.647636
  • Primary Citation Related Structures: 
    3JAB, 3JBQ

  • PubMed Abstract: 

    The cGMP phosphodiesterase of rod photoreceptor cells, PDE6, is the key effector enzyme in phototransduction. Two large catalytic subunits, PDE6α and -β, each contain one catalytic domain and two non-catalytic GAF domains, whereas two small inhibitory PDE6γ subunits allow tight regulation by the G protein transducin. The structure of holo-PDE6 in complex with the ROS-1 antibody Fab fragment was determined by cryo-electron microscopy. The ∼11 Å map revealed previously unseen features of PDE6, and each domain was readily fit with high resolution structures. A structure of PDE6 in complex with prenyl-binding protein (PrBP/δ) indicated the location of the PDE6 C-terminal prenylations. Reconstructions of complexes with Fab fragments bound to N or C termini of PDE6γ revealed that PDE6γ stretches from the catalytic domain at one end of the holoenzyme to the GAF-A domain at the other. Removal of PDE6γ caused dramatic structural rearrangements, which were reversed upon its restoration.


  • Organizational Affiliation
    • From the Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030 and.

Macromolecule Content 

  • Total Structure Weight: 260.03 kDa 
  • Atom Count: 17,450 
  • Modeled Residue Count: 2,210 
  • Deposited Residue Count: 2,306 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IgG1-kappa 2E8 light chainA [auth L],
I [auth l]
214Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
IgG1-kappa 2E8 heavy chainB [auth H],
J [auth h]
220Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
phosphodiesterase 5/6 chimera catalytic domainC [auth B],
F
330Bos taurusMutation(s): 0 
EC: 3.1.4.35
UniProt
Find proteins for P16586 (Bos taurus)
Explore P16586 
Go to UniProtKB:  P16586
Find proteins for Q28156 (Bos taurus)
Explore Q28156 
Go to UniProtKB:  Q28156
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ28156P16586
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
phosphodiesterase 6 gamma subunit inhibitory peptideD,
G [auth X]
18Bos taurusMutation(s): 0 
EC: 3.1.4.35
UniProt
Find proteins for P04972 (Bos taurus)
Explore P04972 
Go to UniProtKB:  P04972
Entity Groups
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UniProt GroupP04972
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
GafB domain of phosphodiesterase 2AE [auth C],
H [auth G]
185Bos taurusMutation(s): 0 
EC: 3.1.4.17
UniProt
Find proteins for P14099 (Bos taurus)
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Entity Groups
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UniProt GroupP14099
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
GafA domain of cone phosphodiesterase 6CK [auth 1],
L [auth 2]
186Bos taurusMutation(s): 0 
EC: 3.1.4.35
UniProt
Find proteins for P52731 (Gallus gallus)
Explore P52731 
Go to UniProtKB:  P52731
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UniProt GroupP52731
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Data collection
  • Version 1.2: 2019-12-18
    Changes: Other
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Refinement description, Structure summary