1IG7 | pdb_00001ig7

Msx-1 Homeodomain/DNA Complex Structure

• PDB DOI: https://doi.org/10.2210/pdb1IG7/pdb
• NAKB: 1IG7

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-04-17 Released: 2001-04-23 
• Deposition Author(s): Hovde, S., Abate-Shen, C., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Msx-1 homeodomain/DNA complex

Hovde, S., Abate-Shen, C., Geiger, J.H.

(2001) Biochemistry 40: 12013-12021

• PubMed: 11580277 
• DOI: https://doi.org/10.1021/bi0108148
• Primary Citation Related Structures: 
  1IG7


• PubMed Abstract: 
  

  The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

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Organizational Affiliation: 
• Michigan State University Chemistry Department, East Lansing Michigan 48824, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.79 kDa 
• Atom Count: 1,219 
• Modeled Residue Count: 87 
• Deposited Residue Count: 87 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeotic protein Msx-1	C [auth A]	58	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P13297 (Mus musculus) Explore P13297  Go to UniProtKB:  P13297
IMPC:  MGI:97168

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*CP*TP*AP*AP*TP*TP*GP*AP*AP*GP*G)-3'	A [auth B]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*CP*CP*TP*TP*CP*AP*AP*TP*TP*AP*GP*TP*GP*AP*C)-3'	B [auth C]	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.6	α = 90
b = 60.96	β = 90
c = 82.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-23 
Deposition Author(s): Hovde, S., Abate-Shen, C., Geiger, J.H.

Revision History  

• Version 1.0: 2001-04-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description