4R4L | pdb_00004r4l

Crystal structure of wt cGMP dependent protein kinase I alpha (PKGI alpha) leucine zipper

• PDB DOI: https://doi.org/10.2210/pdb4R4L/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-19 Released: 2015-09-23 
• Deposition Author(s): Reger, A.S., Guo, E., Yang, M.P., Qin, L., Kim, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Literature

Structures of cGMP-Dependent Protein Kinase (PKG) I alpha Leucine Zippers Reveal an Interchain Disulfide Bond Important for Dimer Stability.

Qin, L., Reger, A.S., Guo, E., Yang, M.P., Zwart, P., Casteel, D.E., Kim, C.

(2015) Biochemistry 54: 4419-4422

• PubMed: 26132214 
• DOI: https://doi.org/10.1021/acs.biochem.5b00572
• Primary Citation Related Structures: 
  4R4L, 4R4M


• PubMed Abstract: 
  

  cGMP-dependent protein kinase (PKG) Iα is a central regulator of smooth muscle tone and vasorelaxation. The N-terminal leucine zipper (LZ) domain dimerizes and targets PKG Iα by interacting with G-kinase-anchoring proteins. The PKG Iα LZ contains C42 that is known to form a disulfide bond upon oxidation and to activate PKG Iα. To understand the molecular details of the PKG Iα LZ and C42-C42' disulfide bond, we determined crystal structures of the PKG Iα wild-type (WT) LZ and C42L LZ. Our data demonstrate that the C42-C42' disulfide bond dramatically stabilizes PKG Iα and that the C42L mutant mimics the oxidized WT LZ structurally.

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Organizational Affiliation: 
• ⊥Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.
@Department of Medicine, University of California at San Diego, La Jolla, California 92093, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.97 kDa 
• Atom Count: 1,141 
• Modeled Residue Count: 143 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase 1	A, B, C	49	Homo sapiens	Mutation(s): 0  Gene Names: PRKG1, PRKG1B, PRKGR1A, PRKGR1B EC: 2.7.11.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens) Explore Q13976  Go to UniProtKB:  Q13976
PHAROS:  Q13976 GTEx:  ENSG00000185532

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEZ	D [auth A], E [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.290 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.926	α = 90
b = 95.926	β = 90
c = 63.805	γ = 120

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-23 
Deposition Author(s): Reger, A.S., Guo, E., Yang, M.P., Qin, L., Kim, C.

Revision History  

• Version 1.0: 2015-09-23
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary