Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 9.48 kDa 
• Atom Count: 573 
• Modelled Residue Count: 62 
• Deposited Residue Count: 77 
• Unique protein chains: 2

 3G7L

Chromodomain of Chp1 in complex with Histone H3K9me3 peptide

• PDB DOI:  https://doi.org/10.2210/pdb3G7L/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-10 Released: 2009-04-21 
• Deposition Author(s): Schalch, T., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 

Literature

High-affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish centromeric heterochromatin

Schalch, T., Job, G., Noffsinger, V.J., Shanker, S., Kuscu, C., Joshua-Tor, L., Partridge, J.F.

(2009) Mol Cell 34: 36-46

• PubMed: 19362535 
• DOI: https://doi.org/10.1016/j.molcel.2009.02.024
• Primary Citation of Related Structures:  
  3G7L


• PubMed Abstract: 
  

In fission yeast, assembly of centromeric heterochromatin requires the RITS complex, which consists of Ago1, Tas3, Chp1, and siRNAs derived from centromeric repeats. Recruitment of RITS to centromeres has been proposed to depend on siRNA-dependent targeting of Ago1 to centromeric sequences. Previously, we demonstrated that methylated lysine 9 of histone H3 (H3K9me) acts upstream of siRNAs during heterochromatin establishment. Our crystal structure of Chp1's chromodomain in complex with a trimethylated lysine 9 H3 peptide reveals extensive sites of contact that contribute to Chp1's high-affinity binding. We found that this high-affinity binding is critical for the efficient establishment of centromeric heterochromatin, but preassembled heterochromatin can be maintained when Chp1's affinity for H3K9me is greatly reduced.

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Organizational Affiliation: 

Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromo domain-containing protein 1	A	61	Schizosaccharomyces pombe	Mutation(s): 0  Gene Names: chp1, SPAC18G6.02c
UniProt
Find proteins for Q10103 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10103  Go to UniProtKB:  Q10103

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1/H3.2	B [auth P]	16	N/A	Mutation(s): 1
UniProt
Find proteins for P09988 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P09988  Go to UniProtKB:  P09988

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.237 
• R-Value Work: 0.196 
• R-Value Observed: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.56	α = 90
b = 41.56	β = 90
c = 87.38	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Schalch, T., Joshua-Tor, L.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations