5FLV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1016/j.cell.2016.01.004

  • 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 bee ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5
A, E, I, M
285Mus musculusMutation(s): 2 
Gene Names: Nkx2-5 (Csx, Nkx-2.5, Nkx2e), Tbx5
Find proteins for P42582 (Mus musculus)
Go to UniProtKB:  P42582
Find proteins for P70326 (Mus musculus)
Go to UniProtKB:  P70326
Entity ID: 2
MoleculeChainsLengthOrganism
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,F,J,N22Mus musculus
Entity ID: 3
MoleculeChainsLengthOrganism
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,G,K,O22Mus musculus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.080α = 90.00
b = 158.620β = 89.95
c = 87.860γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references