1B72

PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation.

Piper, D.E.Batchelor, A.H.Chang, C.P.Cleary, M.L.Wolberger, C.

(1999) Cell 96: 587-597

  • DOI: 10.1016/s0092-8674(00)80662-5
  • Primary Citation of Related Structures:  
    1B72

  • PubMed Abstract: 
  • Hox homeodomain proteins are developmental regulators that determine body plan in a variety of organisms. A majority of the vertebrate Hox proteins bind DNA as heterodimers with the Pbx1 homeodomain protein. We report here the 2.35 A structure of a ternary complex containing a human HoxB1-Pbx1 heterodimer bound to DNA ...

    Hox homeodomain proteins are developmental regulators that determine body plan in a variety of organisms. A majority of the vertebrate Hox proteins bind DNA as heterodimers with the Pbx1 homeodomain protein. We report here the 2.35 A structure of a ternary complex containing a human HoxB1-Pbx1 heterodimer bound to DNA. Heterodimer contacts are mediated by the hexapeptide of HoxB1, which binds in a pocket in the Pbx1 protein formed in part by a three-amino acid insertion in the Pbx1 homeodomain. The Pbx1 DNA-binding domain is larger than the canonical homeodomain, containing an additional alpha helix that appears to contribute to binding of the HoxB1 hexapeptide and to stable binding of Pbx1 to DNA. The structure suggests a model for modulation of Hox DNA binding activity by Pbx1 and related proteins.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry and Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (HOMEOBOX PROTEIN HOX-B1)C [auth A]97Homo sapiensMutation(s): 0 
Gene Names: HOXB-1HOXB1HOX2I
UniProt & NIH Common Fund Data Resources
Find proteins for P14653 (Homo sapiens)
Explore P14653 
Go to UniProtKB:  P14653
PHAROS:  P14653
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PBX1)D [auth B]87Homo sapiensMutation(s): 0 
Gene Names: PBX1PRL
UniProt & NIH Common Fund Data Resources
Find proteins for P40424 (Homo sapiens)
Explore P40424 
Go to UniProtKB:  P40424
PHAROS:  P40424
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3')A [auth D]20N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3')B [auth E]20N/A
      Protein Feature View
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      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.35 Å
      • R-Value Free: 0.277 
      • R-Value Work: 0.243 
      • R-Value Observed: 0.243 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 58.67α = 90
      b = 64.58β = 90
      c = 81.91γ = 90
      Software Package:
      Software NamePurpose
      MLPHAREphasing
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 1999-02-19
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance