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 

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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replication protein A 70 kDa DNA-binding subunit
A, B
123Homo sapiensMutation(s): 1 
Gene Names: RPA1 (REPA1, RPA70)
Find proteins for P27694 (Homo sapiens)
Go to Gene View: RPA1
Go to UniProtKB:  P27694
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3,4 dichlorophenylalanine ATRIP derived peptide
C, D
15Homo sapiensMutation(s): 0 
Gene Names: ATRIP (AGS1)
Find proteins for Q8WXE1 (Homo sapiens)
Go to Gene View: ATRIP
Go to UniProtKB:  Q8WXE1
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ZCL
Query on ZCL
C, D
L-peptide linkingC9 H9 Cl2 N O2PHE
2N2
Query on 2N2
C, D
NON-POLYMERC27 H26 N2 O6 S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/66 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 90.145α = 90.00
b = 46.803β = 120.64
c = 78.792γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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