PDBsum entry 3a03

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protein ligands metals links
Gene regulation PDB id
Protein chain
53 a.a. *
SO4 ×2
Waters ×106
* Residue conservation analysis
PDB id:
Name: Gene regulation
Title: Crystal structure of hox11l1 homeodomain
Structure: T-cell leukemia homeobox protein 2. Chain: a. Fragment: homeobox, residues 162-216. Synonym: homeobox protein hox-11l1, neural crest homeobox p engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: tlx2, hox11l1, ncx. Expressed in: escherichia coli. Expression_system_taxid: 562
1.54Å     R-factor:   0.201     R-free:   0.223
Authors: K.Miyazono,K.Nagata,K.Saigo,T.Kojima,M.Tanokura
Key ref: K.Miyazono et al. (2010). Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless. EMBO J, 29, 1613-1623. PubMed id: 20389279
28-Feb-09     Release date:   09-Mar-10    
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Protein chain
Pfam   ArchSchema ?
O43763  (TLX2_HUMAN) -  T-cell leukemia homeobox protein 2
284 a.a.
53 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     3 terms  


EMBO J 29:1613-1623 (2010)
PubMed id: 20389279  
Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.
K.Miyazono, Y.Zhi, Y.Takamura, K.Nagata, K.Saigo, T.Kojima, M.Tanokura.
To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21106075 R.Torella, E.Moroni, M.Caselle, G.Morra, and G.Colombo (2010).
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes.
  BMC Struct Biol, 10, 42.  
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