3RNY | pdb_00003rny

Crystal structure of human RSK1 C-terminal kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3RNY/pdb

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


• Deposited: 2011-04-24 Released: 2012-04-25 
• Deposition Author(s): Li, D., Fu, T.-M., Nan, J., Su, X.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.238 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the autoinhibition of the C-terminal kinase domain of human RSK1.

Li, D., Fu, T.M., Nan, J., Liu, C., Li, L.F., Su, X.D.

(2012) Acta Crystallogr D Biol Crystallogr 68: 680-685

• PubMed: 22683790 
• DOI: https://doi.org/10.1107/S0907444912007457
• Primary Citation Related Structures: 
  3RNY


• PubMed Abstract: 
  

  p90 ribosomal S6 kinases (RSKs) respond to various mitogen stimuli and comprise two distinct protein kinase domains. The C-terminal kinase domain (CTKD) receives signal from ERK1/2 and adopts an autoinhibitory mechanism. Here, the crystal structure of human RSK1 CTKD is reported at 2.7 Å resolution. The structure shows a standard kinase fold, with the catalytic residues in the ATP-binding cleft orientated in optimal conformations for phosphotransfer. The inactivation of the CTKD is conferred by an extra α-helix (αL), which occupies the substrate-binding groove. In combination with previous knowledge, this structure indicates that activation of RSK1 involves the removal of αL from the substrate-binding groove induced by ERK1/2 phosphorylation.

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Organizational Affiliation: 
• State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.69 kDa 
• Atom Count: 4,068 
• Modeled Residue Count: 535 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase alpha-1	A, B	346	Homo sapiens	Mutation(s): 0  Gene Names: RPS6KA1, MAPKAPK1A, RSK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15418 (Homo sapiens) Explore Q15418  Go to UniProtKB:  Q15418
PHAROS:  Q15418 GTEx:  ENSG00000117676

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.238 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.86	α = 90
b = 143.47	β = 95.77
c = 59.92	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Li, D., Fu, T.-M., Nan, J., Su, X.-D.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description