5T4X | pdb_00005t4x

CRYSTAL STRUCTURE OF PDE6D IN APO-STATE

• PDB DOI: https://doi.org/10.2210/pdb5T4X/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-30 Released: 2018-01-10 
• Deposition Author(s): Qureshi, B.M., Schmidt, A., Scheerer, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Mechanistic insights into the role of prenyl-binding protein PrBP/ delta in membrane dissociation of phosphodiesterase 6.

Qureshi, B.M., Schmidt, A., Behrmann, E., Burger, J., Mielke, T., Spahn, C.M.T., Heck, M., Scheerer, P.

(2018) Nat Commun 9: 90-90

• PubMed: 29311697 
• DOI: https://doi.org/10.1038/s41467-017-02569-y
• Primary Citation Related Structures: 
  5T4X


• PubMed Abstract: 
  

  Isoprenylated proteins are associated with membranes and their inter-compartmental distribution is regulated by solubilization factors, which incorporate lipid moieties in hydrophobic cavities and thereby facilitate free diffusion during trafficking. Here we report the crystal structure of a solubilization factor, the prenyl-binding protein (PrBP/δ), at 1.81 Å resolution in its ligand-free apo-form. Apo-PrBP/δ harbors a preshaped, deep hydrophobic cavity, capacitating apo-PrBP/δ to readily bind its prenylated cargo. To investigate the molecular mechanism of cargo solubilization we analyzed the PrBP/δ-induced membrane dissociation of rod photoreceptor phosphodiesterase (PDE6). The results suggest that PrBP/δ exclusively interacts with the soluble fraction of PDE6. Depletion of soluble species in turn leads to dissociation of membrane-bound PDE6, as both are in equilibrium. This "solubilization by depletion" mechanism of PrBP/δ differs from the extraction of prenylated proteins by the similar folded solubilization factor RhoGDI, which interacts with membrane bound cargo via an N-terminal structural element lacking in PrBP/δ.

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Organizational Affiliation: 
• Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany.
Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany.
Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Cryo Electron Microscopy, Charitéplatz 1, D-10117, Berlin, Germany.
Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Enzyme Kinetics, Charitéplatz 1, D-10117, Berlin, Germany.
Division of Biological & Environmental Sciences & Engineering, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
Research Group Structural Dynamics of Proteins, Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, D-53175, Bonn, Germany.
Institute of Biochemistry-Structural Biochemistry, University of Cologne, Zuelpicher Straße 47, D-50674, Cologne, Germany.
UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195, Berlin, Germany.
Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117, Berlin, Germany. [e-mail].
Charité - Universitätsmedizin Berlin, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117, Berlin, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.54 kDa 
• Atom Count: 1,317 
• Modeled Residue Count: 148 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A	170	Mus musculus	Mutation(s): 0  Gene Names: Pde6d
UniProt
Find proteins for O55057 (Mus musculus) Explore O55057  Go to UniProtKB:  O55057

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.662	α = 90
b = 56.534	β = 90
c = 89.101	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-10 
Deposition Author(s): Qureshi, B.M., Schmidt, A., Scheerer, P.

Revision History  

• Version 1.0: 2018-01-10
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description