4NB3

Crystal structure of RPA70N in complex with a 3,4 dichlorophenylalanine ATRIP derived peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a Potent Stapled Helix Peptide That Binds to the 70N Domain of Replication Protein A.

Frank, A.O.Vangamudi, B.Feldkamp, M.D.Souza-Fagundes, E.M.Luzwick, J.W.Cortez, D.Olejniczak, E.T.Waterson, A.G.Rossanese, O.W.Chazin, W.J.Fesik, S.W.

(2014) J Med Chem 57: 2455-2461

  • DOI: 10.1021/jm401730y
  • Primary Citation of Related Structures:  
    4NB3

  • PubMed Abstract: 
  • Stapled helix peptides can serve as useful tools for inhibiting protein-protein interactions but can be difficult to optimize for affinity. Here we describe the discovery and optimization of a stapled helix peptide that binds to the N-terminal domain of the 70 kDa subunit of replication protein A (RPA70N) ...

    Stapled helix peptides can serve as useful tools for inhibiting protein-protein interactions but can be difficult to optimize for affinity. Here we describe the discovery and optimization of a stapled helix peptide that binds to the N-terminal domain of the 70 kDa subunit of replication protein A (RPA70N). In addition to applying traditional optimization strategies, we employed a novel approach for efficiently designing peptides containing unnatural amino acids. We discovered hot spots in the target protein using a fragment-based screen, identified the amino acid that binds to the hot spot, and selected an unnatural amino acid to incorporate, based on the structure-activity relationships of small molecules that bind to this site. The resulting stapled helix peptide potently and selectively binds to RPA70N, does not disrupt ssDNA binding, and penetrates cells. This peptide may serve as a probe to explore the therapeutic potential of RPA70N inhibition in cancer.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replication protein A 70 kDa DNA-binding subunitA, B123Homo sapiensMutation(s): 1 
Gene Names: RPA1REPA1RPA70
UniProt & NIH Common Fund Data Resources
Find proteins for P27694 (Homo sapiens)
Explore P27694 
Go to UniProtKB:  P27694
PHAROS:  P27694
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
3,4 dichlorophenylalanine ATRIP derived peptideC, D15N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WXE1 (Homo sapiens)
Explore Q8WXE1 
Go to UniProtKB:  Q8WXE1
PHAROS:  Q8WXE1
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ZCL
Query on ZCL
C, DL-PEPTIDE LINKINGC9 H9 Cl2 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/66 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.145α = 90
b = 46.803β = 120.64
c = 78.792γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references