3UXW | pdb_00003uxw

Crystal Structures of an A-T-hook/DNA complex

• PDB DOI: https://doi.org/10.2210/pdb3UXW/pdb
• NAKB: 3UXW

• Classification: DNA/PEPTIDE
• Mutation(s): No 


• Deposited: 2011-12-05 Released: 2012-05-23 
• Deposition Author(s): Fonfria-Subiros, E., Acosta-Reyes, F.J., Saperas, N., Pous, J., Subirana, J.A., Campos, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.277 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structure of a complex of DNA with one AT-hook of HMGA1.

Fonfria-Subiros, E., Acosta-Reyes, F., Saperas, N., Pous, J., Subirana, J.A., Campos, J.L.

(2012) PLoS One 7: e37120-e37120

• PubMed: 22615915 
• DOI: https://doi.org/10.1371/journal.pone.0037120
• Primary Citation Related Structures: 
  3UXW


• PubMed Abstract: 
  

  We present here for the first time the crystal structure of an AT-hook domain. We show the structure of an AT-hook of the ubiquitous nuclear protein HMGA1, combined with the oligonucleotide d(CGAATTAATTCG)(2), which has two potential AATT interacting groups. Interaction with only one of them is found. The structure presents analogies and significant differences with previous NMR studies: the AT-hook forms hydrogen bonds between main-chain NH groups and thymines in the minor groove, DNA is bent and the minor groove is widened.

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Organizational Affiliation: 
• Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.8 kDa 
• Atom Count: 2,297 
• Modeled Residue Count: 134 
• Deposited Residue Count: 136 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A-T hook peptide	I [auth K], J [auth L], K [auth M], L [auth N]	10	N/A	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
dodecamer DNA	A, B, C, D, E, F, G, H	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.277 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.143	α = 90
b = 66.855	β = 111.4
c = 50.052	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Fonfria-Subiros, E., Acosta-Reyes, F.J., Saperas, N., Pous, J., Subirana, J.A., Campos, J.L.

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary