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5nm9

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

Structural highlights

5nm9 is a 4 chain structure with sequence from Homo sapiens and Trichoplax adhaerens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.43Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

B3S7S5_TRIAD

Publication Abstract from PubMed

Smad transcription factors activated by TGF-beta 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-beta 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-beta and BMP pathways.

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 JA, Massague J, Macias MJ Nat Commun. 2017 Dec 12;8(1):2070. doi: 10.1038/s41467-017-02054-6. PMID:29234012^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Martin-Malpartida P, Batet M, Kaczmarska Z, Freier R, Gomes T, Aragon E, Zou Y, Wang Q, Xi Q, Ruiz L, Vea A, Marquez JA, Massague J, Macias MJ. Structural basis for genome wide recognition of 5-bp GC motifs by SMAD transcription factors. Nat Commun. 2017 Dec 12;8(1):2070. doi: 10.1038/s41467-017-02054-6. PMID:29234012 doi:http://dx.doi.org/10.1038/s41467-017-02054-6

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5nm9"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the placozoa Trichoplax adhaerens Smad4-MH1 bound to the GGCGC site.==
-<StructureSection load='5nm9' size='340' side='right' caption='[[5nm9]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
+<StructureSection load='5nm9' size='340' side='right'caption='[[5nm9]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Triad Triad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NM9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nm9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Trichoplax_adhaerens Trichoplax adhaerens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NM9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5mf0|5mf0]], [[5mez|5mez]], [[5mey|5mey]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TRIADDRAFT_30731 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10228 TRIAD])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [https://pdbe.org/5nm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [https://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nm9 OCA], [http://pdbe.org/5nm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nm9 RCSB], [http://www.ebi.ac.uk/pdbsum/5nm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nm9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/B3S7S5_TRIAD B3S7S5_TRIAD]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Triad]]
+[[Category: Homo sapiens]]
-[[Category: Freier, R]]
+[[Category: Large Structures]]
-[[Category: Kaczmarska, Z]]
+[[Category: Trichoplax adhaerens]]
-[[Category: Macias, M J]]
+[[Category: Freier R]]
-[[Category: Marquez, J A]]
+[[Category: Kaczmarska Z]]
-[[Category: Dna complex]]
+[[Category: Macias MJ]]
-[[Category: Smad]]
+[[Category: Marquez JA]]
-[[Category: Transcription]]
-[[Category: Transcription factor]]

5nm9

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Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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