PDB-3jbq: Domain Organization and Conformational Plasticity of the G Protei...

Basic information

• Entry: Database: PDB / ID: 3jbq
• Title: Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6

Components

• (IgG1-kappa 2E8 ...) x 2
• (phosphodiesterase ...) x 2
• GafA domain of cone phosphodiesterase 6C
• GafB domain of phosphodiesterase 2A

• Keywords: HYDROLASE/IMMUNE SYSTEM / Phosphodiesterase / photoreceptor / PDE6 / HYDROLASE-IMMUNE SYSTEM complex

Function / homology

Function:

cGMP effects / Smooth Muscle Contraction / RHOBTB1 GTPase cycle / cyclic-nucleotide phosphodiesterase activity / GMP catabolic process / cellular response to macrophage colony-stimulating factor stimulus / 3',5'-cyclic-GMP phosphodiesterase / cellular response to cGMP / positive regulation of G protein-coupled receptor signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / positive regulation of vascular permeability / ion binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / response to stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / regulation of mitochondrion organization / Ca2+ pathway / positive regulation of epidermal growth factor receptor signaling pathway / photoreceptor outer segment membrane / cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / cGMP-mediated signaling / cGMP catabolic process / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of cAMP-mediated signaling / visual perception / cAMP-mediated signaling / synaptic membrane / photoreceptor disc membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / presynaptic membrane / mitochondrial outer membrane / mitochondrial inner membrane / molecular adaptor activity / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / protein homodimerization activity / zinc ion binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol

Domain/homology:

Retinal cGMP phosphodiesterase, gamma subunit / Retinal cGMP phosphodiesterase, gamma subunit superfamily / Retinal cGMP phosphodiesterase, gamma subunit / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain

Component:

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma / cGMP-dependent 3',5'-cyclic phosphodiesterase / Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' / cGMP-specific 3',5'-cyclic phosphodiesterase

• Biological species: Mus musculus (house mouse); Bos taurus (cattle)
• Method: ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11 Å
• Authors: Zhang, Z. / He, F. / Constantine, R. / Baker, M.L. / Baehr, W. / Schmid, M.F. / Wensel, T.G. / Agosto, M.A.
• Citation: Journal: J Biol Chem / Year: 2015; Title: Domain organization and conformational plasticity of the G protein effector, PDE6.; Authors: Zhixian Zhang / Feng He / Ryan Constantine / Matthew L Baker / Wolfgang Baehr / Michael F Schmid / Theodore G Wensel / Melina A Agosto / ; 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.

History

Deposition	Sep 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 18, 2018	Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2	Dec 18, 2019	Group: Other / Category: atom_sites Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

Assembly

Deposited unit

L: IgG1-kappa 2E8 light chain

H: IgG1-kappa 2E8 heavy chain

B: phosphodiesterase 5/6 chimera catalytic domain

D: phosphodiesterase 6 gamma subunit inhibitory peptide

C: GafB domain of phosphodiesterase 2A

F: phosphodiesterase 5/6 chimera catalytic domain

X: phosphodiesterase 6 gamma subunit inhibitory peptide

G: GafB domain of phosphodiesterase 2A

l: IgG1-kappa 2E8 light chain

h: IgG1-kappa 2E8 heavy chain

1: GafA domain of cone phosphodiesterase 6C

2: GafA domain of cone phosphodiesterase 6C

Summary:

• 260 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	260,032	12
Polymers	260,032	12
Non-polymers	0	0
Water	0	0

1

Summary:

• Idetical with deposited unit
• defined by author

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Components

Phosphodiesterase ... , 2 types, 4 molecules B F D X

#3: Protein

B F phosphodiesterase 5/6 chimera catalytic domain / cGMP-specific 3' / 5'-cyclic phosphodiesterase / cone cGMP-specific 3' / 5'-cyclic phosphodiesterase subunit alpha' chimera

Details:

Mass: 38282.086 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: photoreceptor / Cellular location: disk membrane / Organelle: outer segment / Tissue: retina / References: UniProt: Q28156*PLUS

#4: Protein/peptide

D X phosphodiesterase 6 gamma subunit inhibitory peptide / Retinal rod rhodopsin-sensitive cGMP 3' / 5'-cyclic phosphodiesterase subunit gamma / GMP-PDE gamma

Details:

Mass: 2185.436 Da / Num. of mol.: 2 / Fragment: UNP residues 70-87 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: photoreceptor / Cellular location: disk membrane / Organelle: outer segment / Tissue: retina / References: UniProt: P04972

Protein , 2 types, 4 molecules C G 1 2

#5: Protein

C G GafB domain of phosphodiesterase 2A / cGMP-dependent 3' / 5'-cyclic phosphodiesterase

Details:

Mass: 20671.434 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: photoreceptor / Cellular location: disk membrane / Organelle: outer segment / Tissue: retina / References: UniProt: P14099*PLUS

#6: Protein

1 2 GafA domain of cone phosphodiesterase 6C / cone cGMP-specific 3' / 5'-cyclic phosphodiesterase subunit alpha'

Details:

Mass: 21554.822 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: photoreceptor / Cellular location: disk membrane / Organelle: outer segment / Tissue: retina / References: UniProt: P52731*PLUS

Antibody , 2 types, 4 molecules L l H h

#1: Antibody

L l IgG1-kappa 2E8 light chain

Details:

Mass: 23540.990 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: Ascites fluid

#2: Antibody

H h IgG1-kappa 2E8 heavy chain

Details:

Mass: 23781.471 Da /