10OZ | pdb_000010oz

Structure of PDE5 PDE6 chimera


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structural basis of phosphodiesterase-5 conformational organization revealed by a PDE6/PDE5 Chimera.

Srivastava, D.Singh, S.Yu, C.Boyd, K.Artemyev, N.O.

(2026) J Biological Chem : 111467-111467

  • DOI: https://doi.org/10.1016/j.jbc.2026.111467
  • Primary Citation Related Structures: 
    10OZ

  • PubMed Abstract: 

    Phosphodiesterase 5 (PDE5) plays critical role in the nitric oxide-cGMP signaling pathway. Consequently, PDE5 catalytic site inhibitors are widely used in the treatment of erectile dysfunction and pulmonary arterial hypertension. Despite a wealth of structural data on the individual PDE5 catalytic domain with bound drug molecules, understanding of the structural organization of the full-length enzyme and its allosteric activation by noncatalytic cGMP-binding is lacking. To begin to understand the structural organization of PDE5, we solved a cryo-EM structure of a chimeric PDE enzyme (PDE6C/5) comprised of the regulatory domains of cone PDE6C and the PDE5 catalytic domain. The PDE6C/5 structure revealed the protein in the open state conformation similar to that of PDE6, suggesting a comparable conformation for the cGMP-bound PDE5 molecule. The H- and M-loops outlying the catalytic pocket, which are conformationally variable in the structures of isolated PDE5 catalytic domain, are immobilized in the PDE6/5 chimera via the interaction of the H-loop with a linker helix LH2. Decreased dynamics of these loops may underlie the higher catalytic activities of the full-length PDE5 and PDE6C/5 compared to that of the isolated PDE5 catalytic domain. Furthermore, the PDE6C/5 structure defines the folding requirement of the PDE6 catalytic domain for chaperone-dependent maturation that is important for vision.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biophysics.

Macromolecule Content 

  • Total Structure Weight: 208.96 kDa 
  • Atom Count: 12,147 
  • Modeled Residue Count: 1,493 
  • Deposited Residue Count: 1,814 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase PDE5-PDE6 chimera
A, B
800Bos taurusMutation(s): 0 
Gene Names: PDE6CPDEA2PDE5APDE5
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
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
C, D
107Bos taurusMutation(s): 0 
Gene Names: PDE6GPDEG
EC: 3.1.4.35
UniProt
Find proteins for P04972 (Bos taurus)
Explore P04972 
Go to UniProtKB:  P04972
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04972
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VIA

Query on VIA



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
C22 H30 N6 O4 S
BNRNXUUZRGQAQC-UHFFFAOYSA-N
PCG

Query on PCG



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release