5CSI | pdb_00005csi

S100B-RSK1 crystal structure A'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.250 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition by S100B Protein: MODULATION OF THE EXTRACELLULAR SIGNAL-REGULATED KINASE (ERK) SIGNALING CASCADE IN A CALCIUM-DEPENDENT WAY.

Gogl, G.Alexa, A.Kiss, B.Katona, G.Kovacs, M.Bodor, A.Remenyi, A.Nyitray, L.

(2016) J Biological Chem 291: 11-27

  • DOI: https://doi.org/10.1074/jbc.M115.684928
  • Primary Citation Related Structures: 
    5CSF, 5CSI, 5CSJ, 5CSN

  • PubMed Abstract: 

    Mitogen-activated protein kinases (MAPK) promote MAPK-activated protein kinase activation. In the MAPK pathway responsible for cell growth, ERK2 initiates the first phosphorylation event on RSK1, which is inhibited by Ca(2+)-binding S100 proteins in malignant melanomas. Here, we present a detailed in vitro biochemical and structural characterization of the S100B-RSK1 interaction. The Ca(2+)-dependent binding of S100B to the calcium/calmodulin-dependent protein kinase (CaMK)-type domain of RSK1 is reminiscent of the better known binding of calmodulin to CaMKII. Although S100B-RSK1 and the calmodulin-CAMKII system are clearly distinct functionally, they demonstrate how unrelated intracellular Ca(2+)-binding proteins could influence the activity of the CaMK domain-containing protein kinases. Our crystallographic, small angle x-ray scattering, and NMR analysis revealed that S100B forms a "fuzzy" complex with RSK1 peptide ligands. Based on fast-kinetics experiments, we conclude that the binding involves both conformation selection and induced fit steps. Knowledge of the structural basis of this interaction could facilitate therapeutic targeting of melanomas.


  • Organizational Affiliation
    • From the Department of Biochemistry.

Macromolecule Content 

  • Total Structure Weight: 27.44 kDa 
  • Atom Count: 1,568 
  • Modeled Residue Count: 198 
  • Deposited Residue Count: 239 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein S100-B
A, B
95Homo sapiensMutation(s): 0 
Gene Names: S100B
UniProt & NIH Common Fund Data Resources
Find proteins for P04271 (Homo sapiens)
Explore P04271 
Go to UniProtKB:  P04271
PHAROS:  P04271
GTEx:  ENSG00000160307 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04271
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein S6 kinase alpha-149Homo sapiensMutation(s): 0 
Gene Names: RPS6KA1MAPKAPK1ARSK1
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15418
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.250 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.31α = 90
b = 38.57β = 90
c = 173.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2016-01-13
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description