6D08 | pdb_00006d08

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

• PDB DOI: https://doi.org/10.2210/pdb6D08/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-04-10 Released: 2019-04-10 
• Deposition Author(s): Arora, S., Horne, W.S., Islam, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.252 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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

• PubMed: 31518125 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.65 kDa 
• Atom Count: 1,072 
• Modelled Residue Count: 123 
• Deposited Residue Count: 142 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 1	A, C [auth B]	55	Homo sapiens	Mutation(s): 2  Gene Names: CBX1, CBX
UniProt & NIH Common Fund Data Resources
Find proteins for P83916 (Homo sapiens) Explore P83916  Go to UniProtKB:  P83916
PHAROS:  P83916 GTEx:  ENSG00000108468

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	B [auth C], D	16	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth C], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FQA	B [auth C], D	L-PEPTIDE LINKING	C13 H20 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.252 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.191	α = 76.79
b = 34.052	β = 89.89
c = 35.267	γ = 65.1

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Arora, S., Horne, W.S., Islam, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM123234

Revision History  

• 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