This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6s9s

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Dimerization domain of Xenopus laevis LDB1 in complex with darpin 10

Structural highlights

6s9s is a 2 chain structure with sequence from African clawed frog and Synthetic construct sequences. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	ldb1 (African clawed frog)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LDB1_XENLA] Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. Acts as a coactivator together with otx2 to stimulate lhx1/lim1-mediated activation of the gsc promoter in the Spemann organizer. Acts synergistically with lhx1/lim1 and ssbp in axis formation.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The Chip/LIM-domain binding protein (LDB)-single-stranded DNA-binding protein (SSDP) (ChiLS) complex controls numerous cell-fate decisions in animal cells, by mediating transcription of developmental control genes via remote enhancers. ChiLS is recruited to these enhancers by lineage-specific LIM-domain proteins that bind to its Chip/LDB subunit. ChiLS recently emerged as the core module of the Wnt enhanceosome, a multiprotein complex that primes developmental control genes for timely Wnt responses. ChiLS binds to NPFxD motifs within Pygopus (Pygo) and the Osa/ARID1A subunit of the BAF chromatin remodeling complex, which could synergize with LIM proteins in tethering ChiLS to enhancers. Chip/LDB and SSDP both contain N-terminal dimerization domains that constitute the bulk of their structured cores. Here, we report the crystal structures of these dimerization domains, in part aided by DARPin chaperones. We conducted systematic surface scanning by structure-designed mutations, followed by in vitro and in vivo binding assays, to determine conserved surface residues required for binding between Chip/LDB, SSDP, and Pygo-NPFxD. Based on this, and on the 4:2 (SSDP-Chip/LDB) stoichiometry of ChiLS, we derive a highly constrained structural model for this complex, which adopts a rotationally symmetrical SSDP2-LDB2-SSDP2 architecture. Integrity of ChiLS is essential for Pygo binding, and our mutational analysis places the NPFxD pockets on either side of the Chip/LDB dimer, each flanked by an SSDP dimer. The symmetry and multivalency of ChiLS underpin its function as an enhancer module integrating Wnt signals with lineage-specific factors to operate context-dependent transcriptional switches that are pivotal for normal development and cancer.

Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome.,Renko M, Fiedler M, Rutherford TJ, Schaefer JV, Pluckthun A, Bienz M Proc Natl Acad Sci U S A. 2019 Sep 30. pii: 1912705116. doi:, 10.1073/pnas.1912705116. PMID:31570581^[4]

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

References

↑ Mochizuki T, Karavanov AA, Curtiss PE, Ault KT, Sugimoto N, Watabe T, Shiokawa K, Jamrich M, Cho KW, Dawid IB, Taira M. Xlim-1 and LIM domain binding protein 1 cooperate with various transcription factors in the regulation of the goosecoid promoter. Dev Biol. 2000 Aug 15;224(2):470-85. PMID:10926781 doi:http://dx.doi.org/10.1006/dbio.2000.9778
↑ Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, Kennison JA, Ogryzko VV, Dawid IB, Westphal H. Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development. Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14320-5. doi:, 10.1073/pnas.212532399. Epub 2002 Oct 15. PMID:12381786 doi:http://dx.doi.org/10.1073/pnas.212532399
↑ Agulnick AD, Taira M, Breen JJ, Tanaka T, Dawid IB, Westphal H. Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins. Nature. 1996 Nov 21;384(6606):270-2. PMID:8918878 doi:http://dx.doi.org/10.1038/384270a0
↑ Renko M, Fiedler M, Rutherford TJ, Schaefer JV, Pluckthun A, Bienz M. Rotational symmetry of the structured Chip/LDB-SSDP core module of the Wnt enhanceosome. Proc Natl Acad Sci U S A. 2019 Sep 30. pii: 1912705116. doi:, 10.1073/pnas.1912705116. PMID:31570581 doi:http://dx.doi.org/10.1073/pnas.1912705116

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/6s9s"

@@ Line 3: / Line 3: @@
 <StructureSection load='6s9s' size='340' side='right'caption='[[6s9s]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6s9s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S9S FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6s9s]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S9S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6S9S FirstGlance]. <br>
-</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=6s9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9s OCA], [http://pdbe.org/6s9s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s9s RCSB], [http://www.ebi.ac.uk/pdbsum/6s9s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9s ProSAT]</span></td></tr>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ldb1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</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=6s9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s9s OCA], [http://pdbe.org/6s9s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s9s RCSB], [http://www.ebi.ac.uk/pdbsum/6s9s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s9s ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 21: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: African clawed frog]]
 [[Category: Large Structures]]
+[[Category: Synthetic construct sequences]]
 [[Category: Bienz, M]]
 [[Category: Pluckthun, A]]

6s9s

From Proteopedia

Current revision

Dimerization domain of Xenopus laevis LDB1 in complex with darpin 10

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox