5FLV | pdb_00005flv

Crystal structure of NKX2-5 and TBX5 bound to the Nppa promoter region

• PDB DOI: https://doi.org/10.2210/pdb5FLV/pdb
• NAKB: 5FLV

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-10-28 Released: 2016-02-10 
• Deposition Author(s): Stirnimann, C.U., Glatt, S., Mueller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Luna-Zurita, L., Stirnimann, C.U., Glatt, S., Kaynak, B.L., Thomas, S., Baudin, F., Samee, M.A.H., He, D., Small, E.M., Mileikovsky, M., Nagy, A., Holloway, A.K., Pollard, K.S., Muller, C.W., Bruneau, B.G.

(2016) Cell 164: 999

• PubMed: 26875865 
• DOI: https://doi.org/10.1016/j.cell.2016.01.004
• Primary Citation Related Structures: 
  5FLV


• PubMed Abstract: 
  

  Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation.

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Organizational Affiliation: 
• Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; UJF-EMBL-CNRS UMI 3265, Unit of Virus Host-Cell Interactions, 38042 Grenoble Cedex 9, France.
Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Obstetrics and Gynaecology and Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada.
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany. Electronic address: [e-mail].
Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 186.19 kDa 
• Atom Count: 11,035 
• Modeled Residue Count: 1,077 
• Deposited Residue Count: 1,316 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5	A, D [auth E], G [auth I], J [auth M]	285	Mus musculus	Mutation(s): 2
UniProt
Find proteins for P42582 (Mus musculus) Explore P42582  Go to UniProtKB:  P42582
Find proteins for P70326 (Mus musculus) Explore P70326  Go to UniProtKB:  P70326
UniProt Groups	P70326P42582

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*TP*TP*CP*TP*CP*AP*CP*AP*CP*CP*TP*TP *TP*GP*AP*AP*GP*TP*GP*G)-3'	B, E [auth F], H [auth J], K [auth N]	22	Mus musculus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*CP*AP*CP*TP*TP*CP*AP*AP*AP*GP*GP*TP *GP*TP*GP*AP*GP*AP*AP*G)-3'	C, F [auth G], I [auth K], L [auth O]	22	Mus musculus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	M [auth A], N [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.241 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.08	α = 90
b = 158.62	β = 89.95
c = 87.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Stirnimann, C.U., Glatt, S., Mueller, C.W.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description