2GZK

Structure of a complex of tandem HMG boxes and DNA

• PDB DOI:  https://doi.org/10.2210/pdb2GZK/pdb
• NAKB: 2GZK

• Classification: DNA/STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Rattus rattus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-11 Released: 2006-07-25 
• Deposition Author(s): Stott, K., Tang, G.S., Lee, K.B., Thomas, J.O.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of a Complex of Tandem HMG Boxes and DNA.

Stott, K., Tang, G.S., Lee, K.B., Thomas, J.O.

(2006) J Mol Biol 360: 90-104

• PubMed: 16813837 
• DOI: https://doi.org/10.1016/j.jmb.2006.04.059
• Primary Citation of Related Structures:  
  2GZK


• PubMed Abstract: 
  

The high-mobility group protein HMGB1 contains two tandem DNA-binding HMG box domains, A and B, linked by a short flexible linker that allows the two domains to behave independently in the free protein. There is no structural information on how the linked domains and linker behave when bound to DNA, mainly due to the lack of any DNA-sequence preference of HMGB1. We report the structure determination, by NMR spectroscopy, of a well-defined complex of two tandem HMG boxes bound to a 16 bp oligonucleotide. The protein is an engineered version of the AB di-domain of HMGB1, in which the A box has been replaced by the HMG box of the sequence-specific transcription factor SRY, to give SRY.B. In the SRY.B/DNA complex, both HMG boxes bind in the minor groove and contribute to the overall DNA bending by intercalation of bulky hydrophobic residues between base-pairs; the bends reinforce each other, and the basic linker lies partly in the minor groove. As well as being the first structure of an HMG-box di-domain bound to DNA, this provides the first structure of the B domain of HMGB1 bound to DNA.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.78 kDa 
• Atom Count: 1,986 
• Modelled Residue Count: 191 
• Deposited Residue Count: 191 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Sex-determining region on Y / HMGB1	C [auth A]	159	Homo sapiens, Rattus rattus This entity is chimeric	Mutation(s): 0  Gene Names: SRY
UniProt & NIH Common Fund Data Resources
Find proteins for P63159 (Rattus norvegicus) Explore P63159  Go to UniProtKB:  P63159
Find proteins for Q05066 (Homo sapiens) Explore Q05066  Go to UniProtKB:  Q05066
PHAROS:  Q05066
UniProt Groups	Q05066P63159

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*GP*C)-3'	A [auth B]	16	N/A

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

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  2GZK	Kd: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Currently 2GZK does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2006-07-25 
Deposition Author(s): Stott, K., Tang, G.S., Lee, K.B., Thomas, J.O.

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations