3TMH | pdb_00003tmh

Crystal structure of dual-specific A-kinase anchoring protein 2 in complex with cAMP-dependent protein kinase A type II alpha and PDZK1

• PDB DOI: https://doi.org/10.2210/pdb3TMH/pdb

• Classification: TRANSPORT PROTEIN/SIGNALING PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-31 Released: 2012-09-05 
• Deposition Author(s): Sarma, G.N., Phan, R.H., Sankaran, B., Taylor, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.328 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.273 (Depositor) 

Literature

Differential mode of D-AKAP2 to PKA isoforms: Insights from D-AKAP2 PKA RII PDZK1 ternary complex structure

Sarma, G.N., Phan, R.H., Sankaran, B., Taylor, S.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 20-mer - A8B6C6 

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

Macromolecule Content

• Total Structure Weight: 65.26 kDa 
• Atom Count: 3,553 
• Modelled Residue Count: 471 
• Deposited Residue Count: 588 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)/H(+) exchange regulatory cofactor NHE-RF3	A, E, I	87	Homo sapiens	Mutation(s): 0  Gene Names: PDZK1, CAP70, NHERF3, PDZD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T2W1 (Homo sapiens) Explore Q5T2W1  Go to UniProtKB:  Q5T2W1
PHAROS:  Q5T2W1 GTEx:  ENSG00000174827

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase type II-alpha regulatory subunit	B, C, F, G	48	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkar2a
UniProt
Find proteins for P12368 (Rattus norvegicus) Explore P12368  Go to UniProtKB:  P12368

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A-kinase anchor protein 10, mitochondrial	D, H, J [auth L]	45	Homo sapiens	Mutation(s): 0  Gene Names: AKAP10
UniProt & NIH Common Fund Data Resources
Find proteins for O43572 (Homo sapiens) Explore O43572  Go to UniProtKB:  O43572
PHAROS:  O43572 GTEx:  ENSG00000108599

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.328 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.273 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.472	α = 90
b = 121.472	β = 90
c = 88.282	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-05 
Deposition Author(s): Sarma, G.N., Phan, R.H., Sankaran, B., Taylor, S.S.

Revision History  

• Version 1.0: 2012-09-05
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references