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PDBsum entry 2fmm

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protein ligands Protein-protein interface(s) links
Transcription PDB id
2fmm
Jmol PyMol
Contents
Protein chains
118 a.a. *
68 a.a. *
Ligands
SO4 ×4
Waters ×386
* Residue conservation analysis
PDB id:
2fmm
Name: Transcription
Title: Crystal structure of emsy-hp1 complex
Structure: Protein emsy. Chain: e. Fragment: n-terminal domain. Engineered: yes. Chromobox protein homolog 1. Chain: a, b, c, d. Fragment: chromo shadow domain. Synonym: heterochromatin protein 1 homolog beta, hp1 beta, protein, m31, heterochromatin protein p25, hp1hsbeta, p25be
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: emsy, c11orf30. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: cbx1, cbx. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Pentamer (from PDB file)
Resolution:
1.80Å     R-factor:   0.219     R-free:   0.243
Authors: Y.Huang
Key ref:
Y.Huang et al. (2006). Crystal structure of the HP1-EMSY complex reveals an unusual mode of HP1 binding. Structure, 14, 703-712. PubMed id: 16615912 DOI: 10.1016/j.str.2006.01.007
Date:
09-Jan-06     Release date:   23-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7Z589  (EMSY_HUMAN) -  BRCA2-interacting transcriptional repressor EMSY
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1322 a.a.
118 a.a.*
Protein chains
Pfam   ArchSchema ?
P83916  (CBX1_HUMAN) -  Chromobox protein homolog 1
Seq:
Struc:
185 a.a.
68 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 

 

 
DOI no: 10.1016/j.str.2006.01.007 Structure 14:703-712 (2006)
PubMed id: 16615912  
 
 
Crystal structure of the HP1-EMSY complex reveals an unusual mode of HP1 binding.
Y.Huang, M.P.Myers, R.M.Xu.
 
  ABSTRACT  
 
Heterochromatin protein-1 (HP1) plays an essential role in both the assembly of higher-order chromatin structure and epigenetic inheritance. The C-terminal chromo shadow domain (CSD) of HP1 is responsible for homodimerization and interaction with a number of chromatin-associated nonhistone proteins, including EMSY, which is a BRCA2-interacting protein that has been implicated in the development of breast and ovarian cancer. We have determined the crystal structure of the HP1beta CSD in complex with the N-terminal domain of EMSY at 1.8 A resolution. Surprisingly, the structure reveals that EMSY is bound by two HP1 CSD homodimers, and the binding sequences differ from the consensus HP1 binding motif PXVXL. This structural information expands our understanding of HP1 binding specificity and provides insights into interactions between HP1 homodimers that are likely to be important for heterochromatin formation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure Determination
(A) A section of the MAD-phased electron density map surrounding the ENT-proximal HP1 binding site. The 2.3 map is shown in a filled chicken-wire representation and is contoured at the 1.0s level. The refined model of the EMSY-HP1 CSD complex (stick model) is superimposed onto the map. EMSY, HP1 CSD-A1, and HP1 CSD-A2 molecules are shown with carbon bonds colored yellow, magenta, and red, respectively.
(B) The overall structure of the EMSY-HP1 CSD complex shown in a ribbon representation. One asymmetric unit contains half of the EMSY homodimer, and the other half (shaded) is related by a 2-fold symmetry. EMSY is colored yellow, the ENT-proximal CSD dimer (CSD-A) is shown in magenta (CSD-A1) and red (CSD-A2), and the ENT-distal dimer (CSD-B) is shown in green (CSD-B1) and cyan (CSD-B2).
(C) Superposition of the backbones of CSD-A (red), CSD-B (green), and the HP1 CSD dimer of the HP1-CAF-1 complex (white).
 
  The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 703-712) copyright 2006.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21472955 D.L.Mendez, D.Kim, M.Chruszcz, G.E.Stephens, W.Minor, S.Khorasanizadeh, and S.C.Elgin (2011).
The HP1a disordered C terminus and chromo shadow domain cooperate to select target peptide partners.
  Chembiochem, 12, 1084-1096.
PDB code: 3p7j
21366928 N.J.Brideau, and D.A.Barbash (2011).
Functional conservation of the Drosophila hybrid incompatibility gene Lhr.
  BMC Evol Biol, 11, 57.  
20923397 K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
  Crit Rev Biochem Mol Biol, 45, 488-505.  
19836960 M.Billur, H.D.Bartunik, and P.B.Singh (2010).
The essential function of HP1 beta: a case of the tail wagging the dog?
  Trends Biochem Sci, 35, 115-123.  
19131338 S.Garapaty, C.F.Xu, P.Trojer, M.A.Mahajan, T.A.Neubert, and H.H.Samuels (2009).
Identification and Characterization of a Novel Nuclear Protein Complex Involved in Nuclear Hormone Receptor-mediated Gene Regulation.
  J Biol Chem, 284, 7542-7552.  
18587272 P.G.Park, and H.Lee (2008).
Development of thymic lymphomas in mice disrupted of Brca2 allele in the thymus.
  Exp Mol Med, 40, 339-344.  
18678653 S.Honda, and E.U.Selker (2008).
Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa.
  Mol Cell Biol, 28, 6044-6055.  
  18787609 W.A.van Hattem, R.Carvalho, A.Li, G.J.Offerhaus, and M.Goggins (2008).
Amplification of EMSY Gene in a Subset of Sporadic Pancreatic Adenocarcinomas.
  Int J Clin Exp Pathol, 1, 343-351.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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