3IM3 | pdb_00003im3

Crystal structure of PKA RI alpha dimerization/docking domain

• PDB DOI: https://doi.org/10.2210/pdb3IM3/pdb

• Classification: STRUCTURAL PROTEIN, SIGNALING PROTEIN
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-09 Released: 2010-02-02 
• Deposition Author(s): Sarma, G.N., Kinderman, F.S., Kim, C., von Daake, S., Taylor, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Structure of D-AKAP2:PKA RI Complex: Insights into AKAP Specificity and Selectivity

Sarma, G.N., Kinderman, F.S., Kim, C., von Daake, S., Chen, L., Wang, B.C., Taylor, S.S.

(2010) Structure 18: 155-166

• PubMed: 20159461 
• DOI: https://doi.org/10.1016/j.str.2009.12.012
• Primary Citation Related Structures: 
  3IM3, 3IM4


• PubMed Abstract: 
  

  A-kinase anchoring proteins (AKAPs) regulate cyclic AMP-dependent protein kinase (PKA) signaling in space and time. Dual-specific AKAP 2 (D-AKAP2) binds to the dimerization/docking (D/D) domain of both RI and RII regulatory subunits of PKA with high affinity. Here we have determined the structures of the RIalpha D/D domain alone and in complex with D-AKAP2. The D/D domain presents an extensive surface for binding through a well-formed N-terminal helix, and this surface restricts the diversity of AKAPs that can interact. The structures also underscore the importance of a redox-sensitive disulfide in affecting AKAP binding. An unexpected shift in the helical register of D-AKAP2 compared to the RIIalpha:D-AKAP2 complex structure makes the mode of binding to RIalpha novel. Finally, the comparison allows us to deduce a molecular explanation for the sequence and spatial determinants of AKAP specificity.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, MC 0654, La Jolla, CA 92093, USA.

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)

Macromolecule Content 

• Total Structure Weight: 6.1 kDa 
• Atom Count: 463 
• Modeled Residue Count: 50 
• Deposited Residue Count: 50 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase type I-alpha regulatory subunit	A	50	Bos taurus	Mutation(s): 0  Gene Names: PRKAR1A
UniProt
Find proteins for P00514 (Bos taurus) Explore P00514  Go to UniProtKB:  P00514

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A], C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.122	α = 90
b = 44.122	β = 90
c = 93.036	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Sarma, G.N., Kinderman, F.S., Kim, C., von Daake, S., Taylor, S.S.

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-04-07
  Changes: Derived calculations
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary