6MHA

dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine

• PDB DOI: https://doi.org/10.2210/pdb6MHA/pdb

• Classification: PROTEIN BINDING
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-09-17 Released: 2019-09-25 
• Deposition Author(s): Brustad, E.M., Krone, M.W., Albanese, K.I., Waters, M.L.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.219 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Thermodynamic consequences of Tyr to Trp mutations in the cation-pi-mediated binding of trimethyllysine by the HP1 chromodomain

Krone, M.W., Albanese, K.I., Guseman, A.J., He, C.Q., Lee, G.Y., Houk, K.N., Brustad, E.M., Waters, M.L.

(2020) Chem Sci 11: 3495-3500

• DOI: https://doi.org/10.1039/D0SC00227E

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: isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 7.29 kDa 
• Atom Count: 570 
• Modelled Residue Count: 59 
• Deposited Residue Count: 59 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterochromatin protein 1	A	53	Drosophila melanogaster	Mutation(s): 2  Gene Names: Su(var)205, HP1, CG8409
UniProt
Find proteins for P05205 (Drosophila melanogaster) Explore P05205  Go to UniProtKB:  P05205

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
histone H3 peptide containing trimethyllysine, H3K9me3	B	6	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299  Go to UniProtKB:  P02299

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.219 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.007	α = 90
b = 76.695	β = 90
c = 76.508	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
KYLIN	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Brustad, E.M., Krone, M.W., Albanese, K.I., Waters, M.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM118499

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2020-10-21
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description