2QR7 | pdb_00002qr7

2.0A X-ray structure of C-terminal kinase domain of p90 ribosomal S6 kinase 2: Se-Met derivative

• PDB DOI: https://doi.org/10.2210/pdb2QR7/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-07-27 Released: 2007-12-11 
• Deposition Author(s): Malakhova, M., Tereshko, V., Dong, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Structural basis for activation of the autoinhibitory C-terminal kinase domain of p90 RSK2.

Malakhova, M., Tereshko, V., Lee, S.Y., Yao, K., Cho, Y.-Y., Bode, A., Dong, Z.

(2008) Nat Struct Mol Biol 15: 112-113

• PubMed: 18084304 
• DOI: https://doi.org/10.1038/nsmb1347
• Primary Citation Related Structures: 
  2QR7, 2QR8


• PubMed Abstract: 
  

  The X-ray structure at 2.0-A resolution of the p90 ribosomal S6 kinase 2 C-terminal kinase domain revealed a C-terminal autoinhibitory alphaL-helix that was embedded in the kinase scaffold and determines the inactive kinase conformation. We suggest a mechanism of activation through displacement of the alphaL-helix and rearrangement of the conserved residue Glu500, as well as the reorganization of the T-loop into the active conformation.

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Organizational Affiliation: 
• The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, USA.

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: 38.83 kDa 
• Atom Count: 2,461 
• Modeled Residue Count: 298 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase alpha-3	A	342	Mus musculus	Mutation(s): 1  Gene Names: Rps6ka3, Rps6ka-rs1, Rsk2 EC: 2.7.11.1
UniProt
Find proteins for P18654 (Mus musculus) Explore P18654  Go to UniProtKB:  P18654

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.585	α = 90
b = 46.585	β = 90
c = 293.99	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-11 
Deposition Author(s): Malakhova, M., Tereshko, V., Dong, Z.

Revision History  

• Version 1.0: 2007-12-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary