6C4U

Engineered FHA with Myc-pTBD peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Generating a recombinant phosphothreonine-binding domain for a phosphopeptide of the human transcription factor, c-Myc.

Venegas, L.A.Kall, S.L.Bankole, O.Lavie, A.Kay, B.K.

(2018) N Biotechnol 45: 36-44

  • DOI: 10.1016/j.nbt.2018.05.001
  • Primary Citation of Related Structures:  
    6C4U

  • PubMed Abstract: 
  • Transcription factor c-Myc is an oncoprotein that is regulated at the post-translational level through phosphorylation of two conserved residues, Serine 62 (Ser62) and Threonine 58 (Thr58). A highly specific tool capable of recognizing Myc via pThr58 is needed to monitor activation and localization ...

    Transcription factor c-Myc is an oncoprotein that is regulated at the post-translational level through phosphorylation of two conserved residues, Serine 62 (Ser62) and Threonine 58 (Thr58). A highly specific tool capable of recognizing Myc via pThr58 is needed to monitor activation and localization. Through phage display, we have isolated 10 engineered Forkhead-associated (FHA) domains that selectively bind to a phosphothreonine (pThr)-containing peptide (53-FELLPpTPPLSPS-64) segment of human c-Myc. One domain variant was observed to bind to the Myc-pThr58 peptide with a K D value of 800 nM and had >1000-fold discrimination between the phosphorylated and non-phosphorylated peptide. The crystal structure of the engineered FHA Myc-pThr-binding domain (Myc-pTBD) was solved in complex with its cognate ligand. The Myc-pTBD was observed to be structurally similar to the yeast Rad9 FHA1 domain, except that its β4-β5 and β10-β11 loops form a hydrophobic pocket to facilitate the interaction between the domain and the peptide ligand. The Myc-pTBD's specificity for its cognate ligand was demonstrated to be on a par with 3 commercial polyclonal antibodies, suggesting that this recombinant reagent is a viable alternative to antibodies for monitoring Myc regulation.


    Organizational Affiliation

    Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA. Electronic address: bkay@uic.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Forkhead-associated 1134Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.12.1
UniProt
Find proteins for P22216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22216 
Go to UniProtKB:  P22216
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22216
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Myc-pTBD peptide9Homo sapiensMutation(s): 0 
Gene Names: MYCBHLHE39
UniProt & NIH Common Fund Data Resources
Find proteins for P01106 (Homo sapiens)
Explore P01106 
Go to UniProtKB:  P01106
PHAROS:  P01106
Entity Groups  
UniProt GroupP01106
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
G,
H [auth I],
I [auth H],
J,
K [auth L],
G,
H [auth I],
I [auth H],
J,
K [auth L],
L [auth K]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.18α = 90
b = 72.37β = 90
c = 280.35γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
Cootmodel building
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references