8PNA | pdb_00008pna

transcription factor BARHL2 bound to TAATG DNA sequence

• PDB DOI: https://doi.org/10.2210/pdb8PNA/pdb
• NAKB: 8PNA

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-30 Released: 2024-07-10 
• Deposition Author(s): Morgunova, E., Popov, A., Yin, Y., Taipale, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Interfacial water confers transcription factors with dinucleotide specificity.

Morgunova, E., Nagy, G., Yin, Y., Zhu, F., Nayak, S.P., Xiao, T., Sokolov, I., Popov, A., Laughton, C., Grubmuller, H., Taipale, J.

(2025) Nat Struct Mol Biol 32: 650-661

• PubMed: 39753777 
• DOI: https://doi.org/10.1038/s41594-024-01449-6
• Primary Citation Related Structures: 
  7Z5I, 7Z5K, 8PM5, 8PM7, 8PMC, 8PMF, 8PMN, 8PMV, 8PN4, 8PNA, 8PNC


• PubMed Abstract: 
  

  Transcription factors (TFs) recognize specific bases within their DNA-binding motifs, with each base contributing nearly independently to total binding energy. However, the energetic contributions of particular dinucleotides can deviate strongly from the additive approximation, indicating that some TFs can specifically recognize DNA dinucleotides. Here we solved high-resolution (<1 Å) structures of MYF5 and BARHL2 bound to DNAs containing sets of dinucleotides that have different affinities to the proteins. The dinucleotides were recognized either enthalpically, by an extensive water network that connects the adjacent bases to the TF, or entropically, by a hydrophobic patch that maintained interfacial water mobility. This mechanism confers differential temperature sensitivity to the optimal sites, with implications for thermal regulation of gene expression. Our results uncover the enigma of how TFs can recognize more complex local features than mononucleotides and demonstrate that water-mediated recognition is important for predicting affinities of macromolecules from their sequence.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
Department of Biochemistry, University of Cambridge, Cambridge, UK.
State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
Max Planck School Matter to Life, Heidelberg, Germany.
ESRF Grenoble, Grenoble, France.
School of Pharmacy and Biodiscovery Institute, University of Nottingham, Nottingham, UK.
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. [e-mail].
Department of Biochemistry, University of Cambridge, Cambridge, UK. [e-mail].
Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland. [e-mail].
Generative and Synthetic Genomics Programme, Wellcome Sanger Institute, Hinxton, UK. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 15.48 kDa 
• Atom Count: 1,362 
• Modeled Residue Count: 91 
• Deposited Residue Count: 91 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BarH-like 2 homeobox protein	B [auth A]	67	Homo sapiens	Mutation(s): 0  Gene Names: BARHL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY43 (Homo sapiens) Explore Q9NY43  Go to UniProtKB:  Q9NY43
PHAROS:  Q9NY43 GTEx:  ENSG00000143032

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA	A [auth B]	12	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	C [auth D]	12	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.853	α = 90
b = 46.881	β = 90
c = 71.758	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Morgunova, E., Popov, A., Yin, Y., Taipale, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2025-01-15
  Changes: Database references, Structure summary
• Version 1.2: 2025-04-23
  Changes: Database references