4I7B | pdb_00004i7b

Siah1 bound to synthetic peptide (ACE)KLRPV(ABA)MVRPTVR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4I7B

This is version 1.3 of the entry. See complete history

Literature

Structure-based design of covalent siah inhibitors.

Stebbins, J.L.Santelli, E.Feng, Y.De, S.K.Purves, A.Motamedchaboki, K.Wu, B.Ronai, Z.A.Liddington, R.C.Pellecchia, M.

(2013) Chem Biol 20: 973-982

  • DOI: https://doi.org/10.1016/j.chembiol.2013.06.008
  • Primary Citation Related Structures: 
    4I7B, 4I7C, 4I7D

  • PubMed Abstract: 

    The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry, and functional data demonstrate that these peptide mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in the cell. The proposed strategy may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions.


  • Organizational Affiliation
    • Signal Transduction Program and Cell Death Program, Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 47.35 kDa 
  • Atom Count: 3,141 
  • Modeled Residue Count: 398 
  • Deposited Residue Count: 420 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase SIAH1
A, C
196Homo sapiensMutation(s): 0 
Gene Names: SIAH1HUMSIAH
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUQ4 (Homo sapiens)
Explore Q8IUQ4 
Go to UniProtKB:  Q8IUQ4
PHAROS:  Q8IUQ4
GTEx:  ENSG00000196470 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IUQ4
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein phyllopod
B, D
14Drosophila melanogasterMutation(s): 1 
UniProt
Find proteins for Q27934 (Drosophila melanogaster)
Explore Q27934 
Go to UniProtKB:  Q27934
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27934
Sequence Annotations
Expand
Reference Sequence

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.745α = 90
b = 87.913β = 100.59
c = 59.884γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection