4QXK | pdb_00004qxk

Joint X-ray/neutron structure of PKGIbeta in complex with cGMP

• PDB DOI: https://doi.org/10.2210/pdb4QXK/pdb

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


• Deposited: 2014-07-21 Released: 2014-11-12 
• Deposition Author(s): Kim, C., Gerlits, O., Kovalevsky, A., Huang, G.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• R-Value Free: 
  0.263 (DCC) 
• R-Value Work: 
  0.249 (DCC) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.318 (Depositor) 
• R-Value Work: 
  0.277 (Depositor) 
• R-Value Observed: 
  0.277 (Depositor) 

Literature

Neutron Diffraction Reveals Hydrogen Bonds Critical for cGMP-Selective Activation: Insights for cGMP-Dependent Protein Kinase Agonist Design.

Huang, G.Y., Gerlits, O.O., Blakeley, M.P., Sankaran, B., Kovalevsky, A.Y., Kim, C.

(2014) Biochemistry 53: 6725-6727

• PubMed: 25271401 
• DOI: https://doi.org/10.1021/bi501012v
• Primary Citation Related Structures: 
  4QX5, 4QXK


• PubMed Abstract: 
  

  High selectivity of cyclic-nucleotide binding (CNB) domains for cAMP and cGMP are required for segregating signaling pathways; however, the mechanism of selectivity remains unclear. To investigate the mechanism of high selectivity in cGMP-dependent protein kinase (PKG), we determined a room-temperature joint X-ray/neutron (XN) structure of PKG Iβ CNB-B, a domain 200-fold selective for cGMP over cAMP, bound to cGMP (2.2 Å), and a low-temperature X-ray structure of CNB-B with cAMP (1.3 Å). The XN structure directly describes the hydrogen bonding interactions that modulate high selectivity for cGMP, while the structure with cAMP reveals that all these contacts are disrupted, explaining its low affinity for cAMP.

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Organizational Affiliation: 
• Verna and Mars McClean Department of Biochemistry and Molecular Biology, Baylor College of Medicine , One Baylor Plaza, Houston, Texas 77004, United States.

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: 17.31 kDa 
• Atom Count: 1,138 
• Modeled Residue Count: 127 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase 1	A	153	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
PCG	B [auth A]	CYCLIC GUANOSINE MONOPHOSPHATE C10 H12 N5 O7 P ZOOGRGPOEVQQDX-UUOKFMHZSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• R-Value Free:  0.263 (DCC) 
• R-Value Work:  0.249 (DCC) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.318 (Depositor) 
• R-Value Work:  0.277 (Depositor) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.746	α = 90
b = 48.746	β = 90
c = 104.861	γ = 90

Software Package:

Software Name	Purpose
nCNS	refinement
Maatel	data collection
HKL-3000	data reduction
LAUEGEN	data reduction
HKL-3000	data scaling
LSCALE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Kim, C., Gerlits, O., Kovalevsky, A., Huang, G.Y.

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations