5NM9 | pdb_00005nm9

Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.

• PDB DOI: https://doi.org/10.2210/pdb5NM9/pdb
• NAKB: 5NM9

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


• Deposited: 2017-04-05 Released: 2017-11-15 
• Deposition Author(s): Kaczmarska, Z., Freier, R., Marquez, J.A., Macias, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.251 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.221 (Depositor) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors.

Martin-Malpartida, P., Batet, M., Kaczmarska, Z., Freier, R., Gomes, T., Aragon, E., Zou, Y., Wang, Q., Xi, Q., Ruiz, L., Vea, A., Marquez, J.A., Massague, J., Macias, M.J.

(2017) Nat Commun 8: 2070-2070

• PubMed: 29234012 
• DOI: https://doi.org/10.1038/s41467-017-02054-6
• Primary Citation Related Structures: 
  5MEY, 5MEZ, 5MF0, 5NM9, 5OD6, 5ODG


• PubMed Abstract: 
  

  Smad transcription factors activated by TGF-β or by BMP receptors form trimeric complexes with Smad4 to target specific genes for cell fate regulation. The CAGAC motif has been considered as the main binding element for Smad2/3/4, whereas Smad1/5/8 have been thought to preferentially bind GC-rich elements. However, chromatin immunoprecipitation analysis in embryonic stem cells showed extensive binding of Smad2/3/4 to GC-rich cis-regulatory elements. Here, we present the structural basis for specific binding of Smad3 and Smad4 to GC-rich motifs in the goosecoid promoter, a nodal-regulated differentiation gene. The structures revealed a 5-bp consensus sequence GGC(GC)|(CG) as the binding site for both TGF-β and BMP-activated Smads and for Smad4. These 5GC motifs are highly represented as clusters in Smad-bound regions genome-wide. Our results provide a basis for understanding the functional adaptability of Smads in different cellular contexts, and their dependence on lineage-determining transcription factors to target specific genes in TGF-β and BMP pathways.

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Organizational Affiliation: 
• Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
EMBL Grenoble, 71 Avenue des Martyrs, CS 90181, 38042, Grenoble, Cedex 9, France.
Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
Center for the Science of Therapeutics, Broad Institute of MIT and Harvard , 415 Main St, Cambridge, MA, 02142, USA.
MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain. [e-mail].
ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 43.14 kDa 
• Atom Count: 2,656 
• Modeled Residue Count: 281 
• Deposited Residue Count: 322 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mothers against decapentaplegic homolog	A, B	143	Trichoplax adhaerens	Mutation(s): 0  Gene Names: TRIADDRAFT_30731
UniProt
Find proteins for B3S7S5 (Trichoplax adhaerens) Explore B3S7S5  Go to UniProtKB:  B3S7S5

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.251 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.221 (Depositor) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.15	α = 90
b = 76.98	β = 90
c = 145.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Kaczmarska, Z., Freier, R., Marquez, J.A., Macias, M.J.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description