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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
R-Value Free:
0.260 (DCC)
R-Value Work:
0.250 (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)

wwPDB Validation 3D Report Full Report

👁 Image

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens) Explore Q13976 Go to UniProtKB: Q13976
PHAROS: Q13976 GTEx: ENSG00000185532
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13976
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCG Query on PCG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CYCLIC GUANOSINE MONOPHOSPHATE C₁₀ H₁₂ N₅ O₇ P ZOOGRGPOEVQQDX-UUOKFMHZSA-N	👁 Image	Focus chain B [auth A] Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N	👁 Image	Focus chain C [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
R-Value Free: 0.260 (DCC)
R-Value Work: 0.250 (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

View Full Validation Report

👁 Image

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Revision History (Full details and data files)

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