5FLV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.196 

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
  • Primary Citation of 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 ...

    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; 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: benoit.bruneau@gladstone.ucsf.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOMEOBOX PROTEIN NKX-2.5, T-BOX TRANSCRIPTION FACTOR TBX5A,
D [auth E],
G [auth I],
J [auth M]
285Mus musculusMutation(s): 2 
Gene Names: Nkx2-5CsxNkx-2.5Nkx2eTbx5
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42582P70326
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
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]
22Mus musculus
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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]
22Mus musculus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
M [auth A],
N [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.08α = 90
b = 158.62β = 89.95
c = 87.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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