4QR9

Crystal structure of two HMGB1 Box A domains cooperating to underwind and kink a DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 1.2 of the entry. See complete history


Literature

Two high-mobility group box domains act together to underwind and kink DNA.

Sanchez-Giraldo, R.Acosta-Reyes, F.J.Malarkey, C.S.Saperas, N.Churchill, M.E.Campos, J.L.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1423-1432

  • DOI: 10.1107/S1399004715007452
  • Primary Citation of Related Structures:  
    4QR9

  • PubMed Abstract: 
  • High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA ...

    High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1-DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.


    Organizational Affiliation

    Departament d'Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High mobility group protein B1A, B76Rattus norvegicusMutation(s): 0 
Gene Names: Hmgb1Hmg-1Hmg1
UniProt
Find proteins for P63159 (Rattus norvegicus)
Explore P63159 
Go to UniProtKB:  P63159
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63159
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')C, D, E, F10synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.751α = 90
b = 84.17β = 90
c = 94.227γ = 90
Software Package:
Software NamePurpose
Xalocdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Database references
  • Version 1.2: 2015-07-29
    Changes: Database references, Experimental preparation, Source and taxonomy