8XAG | pdb_00008xag

Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone H3.3K27me3 peptide

• PDB DOI: https://doi.org/10.2210/pdb8XAG/pdb

• Classification: GENE REGULATION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-04 Released: 2024-12-04 
• Deposition Author(s): Liu, Y., Huang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.250 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the chromodomain of Arabidopsis LHP1 in complex with histone H3.3K27me3 peptide

Liu, Y., Huang, Y.

To be published.

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

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: 17.12 kDa 
• Atom Count: 1,269 
• Modeled Residue Count: 132 
• Deposited Residue Count: 148 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromo domain-containing protein LHP1	A, B	66	Arabidopsis thaliana	Mutation(s): 0  Gene Names: LHP1
UniProt
Find proteins for Q946J8 (Arabidopsis thaliana) Explore Q946J8  Go to UniProtKB:  Q946J8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
histone H3.3K27me3 peptide	C, D	8	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59169 (Arabidopsis thaliana) Explore P59169  Go to UniProtKB:  P59169

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.250 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.37	α = 90
b = 90.623	β = 90
c = 63.574	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Liu, Y., Huang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171186

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release