Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33783.44 
• Atom Count: 1949 
• Residue Count: 224 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1B72

PBX1, HOMEOBOX PROTEIN HOX-B1/DNA TERNARY COMPLEX

• DOI: 10.2210/pdb1B72/pdb
• NDB: PD0075

• Classification: PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 1999-01-27 Released: 1999-02-19 
• Deposition Author(s): Piper, D.E., Batchelor, A.H., Chang, C.-P., Cleary, M.L., Wolberger, C.

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Experimental Data Snapshot

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

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: 10052460 


• 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. 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (HOMEOBOX PROTEIN HOX-B1)	A	97	Homo sapiens	Mutation(s): 0  Gene Names: HOXB1 (HOX2I)
Find proteins for P14653 (Homo sapiens) Go to Gene View: HOXB1 Go to UniProtKB:  P14653

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PROTEIN (PBX1)	B	87	Homo sapiens	Mutation(s): 0  Gene Names: PBX1 (PRL)
Find proteins for P40424 (Homo sapiens) Go to Gene View: PBX1 Go to UniProtKB:  P40424

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (5'-D(*AP*CP*TP*CP*TP*AP*TP*GP*AP*TP*TP*GP*AP*TP*CP*GP*GP*CP*TP*G)-3')	D	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*TP*CP*AP*GP*CP*CP*GP*AP*TP*CP*AP*AP*TP*CP*AP*TP*AP*GP*AP*G)-3')	E	20	N/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 = 58.670	α = 90.00
b = 64.580	β = 90.00
c = 81.910	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
MLPHARE	phasing
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-27 
• Released Date: 1999-02-19 
• Deposition Author(s): Piper, D.E., Batchelor, A.H., Chang, C.-P., Cleary, M.L., Wolberger, C.

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