6D08

Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Engineering Methyllysine Writers and Readers for Allele-Specific Regulation of Protein-Protein Interactions.

Arora, S.Horne, W.S.Islam, K.

(2019) J Am Chem Soc 141: 15466-15470

  • DOI: https://doi.org/10.1021/jacs.9b05725
  • Primary Citation of Related Structures:  
    6D07, 6D08

  • PubMed Abstract: 

    Protein-protein interactions mediated by methyllysine are ubiquitous in biological systems. Specific perturbation of such interactions has remained a challenging endeavor. Herein, we describe an allele-specific strategy toward an engineered protein-protein interface orthogonal to the human proteome. We develop a methyltransferase (writer) variant that installs aryllysine moiety on histones that can only be recognized by an engineered chromodomain (reader). We establish biochemical integrity of the engineered interface, provide structural evidence for orthogonality and validate its applicability to identify transcriptional regulators. Our approach provides an unprecedented strategy for specific manipulation of the methyllysine interactome.


  • Organizational Affiliation

    Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromobox protein homolog 1A,
C [auth B]
55Homo sapiensMutation(s): 2 
Gene Names: CBX1CBX
UniProt & NIH Common Fund Data Resources
Find proteins for P83916 (Homo sapiens)
Explore P83916 
Go to UniProtKB:  P83916
PHAROS:  P83916
GTEx:  ENSG00000108468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83916
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1B [auth C],
D
16Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.191α = 76.79
b = 34.052β = 89.89
c = 35.267γ = 65.1
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM123234

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection, Derived calculations