1LFU | pdb_00001lfu

NMR Solution Structure of the Extended PBX Homeodomain Bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb1LFU/pdb
• NAKB: 1LFU
• BMRB: 5349

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-04-12 Released: 2003-01-14 
• Deposition Author(s): Sprules, T., Green, N., Featherstone, M., Gehring, K.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: lowest energy with acceptable geometry 

Literature

Lock and Key Binding of the HOX YPWM Peptide to the PBX Homeodomain

Sprules, T., Green, N., Featherstone, M., Gehring, K.

(2003) J Biological Chem 278: 1053-1058

• PubMed: 12409300 
• DOI: https://doi.org/10.1074/jbc.M207504200
• Primary Citation Related Structures: 
  1LFU


• PubMed Abstract: 
  

  HOX homeodomain proteins bind short core DNA sequences to control very specific developmental processes. DNA binding affinity and sequence selectivity are increased by the formation of cooperative complexes with the PBX homeodomain protein. A conserved YPWM motif in the HOX protein is necessary for cooperative binding with PBX. We have determined the structure of a PBX homeodomain bound to a 14-mer DNA duplex. A relaxation-optimized procedure was developed to measure DNA residual dipolar couplings at natural abundance in the 20-kDa binary complex. When the PBX homeodomain binds to DNA, a fourth alpha-helix is formed in the homeodomain. This helix rigidifies the DNA recognition helix of PBX and forms a hydrophobic binding site for the HOX YPWM peptide. The HOX peptide itself shows some structure in solution and suggests that the interaction between PBX and HOX is an example of "lock and key" binding. The NMR structure explains the requirement of DNA for the PBX-HOX interaction and the increased affinity of DNA binding.

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Organizational Affiliation: 
• Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.14 kDa 
• Atom Count: 1,244 
• Modeled Residue Count: 110 
• Deposited Residue Count: 110 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
homeobox protein PBX1	C [auth P]	82	Mus musculus	Mutation(s): 1  Gene Names: PBX1
UniProt
Find proteins for P41778 (Mus musculus) Explore P41778  Go to UniProtKB:  P41778

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3'	A	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3'	B	14	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: lowest energy with acceptable geometry 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Sprules, T., Green, N., Featherstone, M., Gehring, K.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2021-10-27
  Changes: Data collection, Database references
• Version 1.5: 2024-05-22
  Changes: Data collection