5E8F

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D

• PDB DOI: https://doi.org/10.2210/pdb5E8F/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-14 Released: 2015-11-18 
• Deposition Author(s): Fansa, E.K., O'Reilly, N.J., Ismail, S.A., Wittinghofer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

The N- and C-terminal ends of RPGR can bind to PDE6 delta.

Fansa, E.K., O'Reilly, N.J., Ismail, S., Wittinghofer, A.

(2015) EMBO Rep 16: 1583-1585

• PubMed: 26553937 
• DOI: https://doi.org/10.15252/embr.201541404
• Primary Citation of Related Structures:  
  5E8F


• PubMed Abstract: 
  

  This study shows that the prenylated C‐terminus of RPGR can bind to PDE6δ with high affinity, suggesting two distinct binding sites of the RPGR/PDE6δ complex. The serine residue at the −3 position relative to the prenylated cysteine seems to play a key role in defining the selectivity of PDE6δ towards ciliary prenylated cargo. [Image: see text]

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Organizational Affiliation: 

Max Planck Institute of Molecular Physiology, Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.33 kDa 
• Atom Count: 2,651 
• Modelled Residue Count: 306 
• Deposited Residue Count: 308 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta	A, B [auth C]	149	Homo sapiens	Mutation(s): 0  Gene Names: PDE6D, PDED EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens) Explore O43924  Go to UniProtKB:  O43924
PHAROS:  O43924 GTEx:  ENSG00000156973

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'	C [auth D], D [auth E]	5	Homo sapiens	Mutation(s): 0  Gene Names: PDE6C, PDEA2 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for P51160 (Homo sapiens) Explore P51160  Go to UniProtKB:  P51160
PHAROS:  P51160 GTEx:  ENSG00000095464

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GER	E [auth D], F [auth E]	GERAN-8-YL GERAN C20 H34 HSOYJGBJQAKCNA-CAIKYXSQSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMT	C [auth D], D [auth E]	L-PEPTIDE LINKING	C4 H9 N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.71	α = 90
b = 81.43	β = 90
c = 118.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Fansa, E.K., O'Reilly, N.J., Ismail, S.A., Wittinghofer, A.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description