Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37.40 kDa 
• Atom Count: 2066 
• Modelled Residue Count: 254 
• Deposited Residue Count: 327 
• Unique protein chains: 1

3A61

Crystal structure of unphosphorylated p70S6K1 (Form II)

• PDB DOI: 10.2210/pdb3A61/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-08-18 Released: 2009-10-27 
• Deposition Author(s): Sunami, T., Byrne, N., Diehl, R.E., Funabashi, K., Hall, D.L., Ikuta, M., Patel, S.B., Shipman, J.M., Smith, R.F., Takahashi, I., Zugay-Murphy, J., Iwasawa, Y., Lumb, K.J., Munshi, S.K., Sharma, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 0.349 
• R-Value Work: 0.265 
• R-Value Observed: 0.274 

Literature

Structural basis of human p70 ribosomal S6 kinase-1 regulation by activation loop phosphorylation.

Sunami, T., Byrne, N., Diehl, R.E., Funabashi, K., Hall, D.L., Ikuta, M., Patel, S.B., Shipman, J.M., Smith, R.F., Takahashi, I., Zugay-Murphy, J., Iwasawa, Y., Lumb, K.J., Munshi, S.K., Sharma, S.

(2010) J Biol Chem 285: 4587-4594

• PubMed: 19864428 
• DOI: 10.1074/jbc.M109.040667
• Primary Citation of Related Structures:  
  3A60, 3A61, 3A62


• PubMed Abstract: 
  

p70 ribosomal S6 kinase (p70S6K) is a downstream effector of the mTOR signaling pathway involved in cell proliferation, cell growth, cell-cycle progression, and glucose homeostasis. Multiple phosphorylation events within the catalytic, autoinhibitory, and hydrophobic motif domains contribute to the regulation of p70S6K. We report the crystal structures of the kinase domain of p70S6K1 bound to staurosporine in both the unphosphorylated state and in the 3'-phosphoinositide-dependent kinase-1-phosphorylated state in which Thr-252 of the activation loop is phosphorylated. Unphosphorylated p70S6K1 exists in two crystal forms, one in which the p70S6K1 kinase domain exists as a monomer and the other as a domain-swapped dimer. The crystal structure of the partially activated kinase domain that is phosphorylated within the activation loop reveals conformational ordering of the activation loop that is consistent with a role in activation. The structures offer insights into the structural basis of the 3'-phosphoinositide-dependent kinase-1-induced activation of p70S6K and provide a platform for the rational structure-guided design of specific p70S6K inhibitors.

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Organizational Affiliation: 

Department of Chemistry, Tsukuba Research Institute, Banyu Pharmaceutical Company, Limited, Tsukuba, Ibaraki, 300-2611, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S6 kinase beta-1	A	327	Homo sapiens	Mutation(s): 0  Gene Names: RPS6KB1, STK14A EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P23443 (Homo sapiens) Explore P23443  Go to UniProtKB:  P23443
PHAROS:  P23443 GTEx:  ENSG00000108443

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU	B [auth A]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.43 Å
• R-Value Free: 0.349 
• R-Value Work: 0.265 
• R-Value Observed: 0.274 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.636	α = 90
b = 63.014	β = 90
c = 98.349	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-18 
• Released Date: 2009-10-27 
Deposition Author(s): Sunami, T., Byrne, N., Diehl, R.E., Funabashi, K., Hall, D.L., Ikuta, M., Patel, S.B., Shipman, J.M., Smith, R.F., Takahashi, I., Zugay-Murphy, J., Iwasawa, Y., Lumb, K.J., Munshi, S.K., Sharma, S.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance