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 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


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.,Sect.D 71: 1423-1432

  • DOI: 10.1107/S1399004715007452

  • 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 rem ...

    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 LengthOrganismDetails
High mobility group protein B1
A, B
76Rattus norvegicusMutation(s): 0 
Gene Names: Hmgb1 (Hmg-1, Hmg1)
Find proteins for P63159 (Rattus norvegicus)
Go to UniProtKB:  P63159
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*AP*TP*CP*GP*AP*TP*AP*T)-3')C,D,E,F10synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.751α = 90.00
b = 84.170β = 90.00
c = 94.227γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
Xalocdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

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