7Z5K | pdb_00007z5k

Transcription factor MYF5 bound to non-symmetrical site

• PDB DOI: https://doi.org/10.2210/pdb7Z5K/pdb
• NAKB: 7Z5K

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


• Deposited: 2022-03-09 Released: 2023-03-22 
• 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: 2.28 Å
• R-Value Free: 
  0.266 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.231 (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 

• 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.81 kDa 
• Atom Count: 1,775 
• Modeled Residue Count: 148 
• Deposited Residue Count: 150 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myogenic factor 5	A, B	57	Homo sapiens	Mutation(s): 0  Gene Names: MYF5, BHLHC2
UniProt & NIH Common Fund Data Resources
Find proteins for P13349 (Homo sapiens) Explore P13349  Go to UniProtKB:  P13349
PHAROS:  P13349 GTEx:  ENSG00000111049

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*GP*CP*AP*AP*CP*AP*GP*CP*TP*GP*AP*CP*GP*CP*GP*T)-3')	C [auth E]	18	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*CP*GP*TP*CP*AP*GP*CP*TP*GP*TP*TP*GP*CP*GP*C)-3')	D [auth F]	18	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.266 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.443	α = 90
b = 33.839	β = 91.88
c = 53.541	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
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: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.2: 2025-01-15
  Changes: Database references, Structure summary