6NJQ | pdb_00006njq

Structure of TBP-Hoogsteen containing DNA complex

• PDB DOI: https://doi.org/10.2210/pdb6NJQ/pdb
• NAKB: 6NJQ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Arabidopsis thaliana, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-04 Released: 2019-10-30 
• Deposition Author(s): Schumacher, M.A., Stelling, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.278 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Infrared Spectroscopic Observation of a G-C+Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.

Stelling, A.L., Liu, A.Y., Zeng, W., Salinas, R., Schumacher, M.A., Al-Hashimi, H.M.

(2019) Angew Chem Int Ed Engl 58: 12010-12013

• PubMed: 31268220 
• DOI: https://doi.org/10.1002/anie.201902693
• Primary Citation Related Structures: 
  6NJQ


• PubMed Abstract: 
  

  Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson-Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X-ray structures of protein-DNA complexes. However, there are several examples of Hoogsteen bps in crystal structures that form Watson-Crick bps when examined under solution conditions. Furthermore, Hoogsteen bps can sometimes be difficult to resolve in DNA:protein complexes by X-ray crystallography due to ambiguous electron density and by solution-state NMR spectroscopy due to size limitations. Here, using infrared spectroscopy, we report the first direct solution-state observation of a Hoogsteen (G-C ⁺ ) bp in a DNA:protein complex under solution conditions with specific application to DNA-bound TATA-box binding protein. These results support a previous assignment of a G-C ⁺ Hoogsteen bp in the complex, and indicate that Hoogsteen bps do indeed exist under solution conditions in DNA:protein complexes.

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Organizational Affiliation: 
• Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
Department of Chemistry, Duke University, Durham, NC, 27710, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 66.26 kDa 
• Atom Count: 4,112 
• Modeled Residue Count: 430 
• Deposited Residue Count: 496 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TATA-box-binding protein 1	A [auth B], D [auth A]	220	Arabidopsis thaliana	Mutation(s): 0  Gene Names: TBP1, At3g13445, MRP15.10
UniProt
Find proteins for P28147 (Arabidopsis thaliana) Explore P28147  Go to UniProtKB:  P28147

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*AP*CP*GP*GP*GP*CP*A)-3')	B [auth E], E [auth C]	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*TP*AP*GP*C)-3')	C [auth F], F [auth D]	14	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.278 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.299	α = 90
b = 57.967	β = 96.5
c = 149.752	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Schumacher, M.A., Stelling, A.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description