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 

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


  • 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 t ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (HOMEOBOX PROTEIN HOX-B1)
A
97Homo sapiensGene Names: HOXB1 (HOX2I)
Find proteins for P14653 (Homo sapiens)
Go to Gene View: HOXB1
Go to UniProtKB:  P14653
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PBX1)
B
87Homo sapiensGene Names: PBX1 (PRL)
Find proteins for P40424 (Homo sapiens)
Go to Gene View: PBX1
Go to UniProtKB:  P40424
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3')D20N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3')E20N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.670α = 90.00
b = 64.580β = 90.00
c = 81.910γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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