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Model of the complex between zinc finger 5 of MyT1 and DNA

[ PDB file ] [ PubMed link ]

We have used a variety of NMR, mutagenesis and binding data to build a model of the interaction between zinc finger 5 from the neuronal transcription factor MyT1 and its cognate DNA site. The model was built using the HADDOCK data-driven docking software (from Alexandre Bonvin) and shows that the domain fits snugly into the DNA major groove, making a number of base specific hydrogen bonds and hydrophobic contacts.

The structure of an Lhx3-Ldb1 complex

[ PDB file ] [ PubMed link ]

In developing V2 interneurons (and various other tissues) the LIM domains of Lhx3 must contact the LIM-interaction domain of Ldb1 as part of a transcription complex that specifies the cell type. This is how they do it. The Lhx3 is in blue and Ldb1-LID is in gold.

The crystal structure of a complex between two LIM-homeodomain proteins

[ PDB file ] [ PubMed link ]

In developing motor neurons Isl1 displaces Lhx3 as the binding partner of the essential LIM-HD cofactor protein Ldb1. Isl1 provides Lhx3 with a decoy binding domain from a region in the C-terminus of Isl1 that, despite very low sequence identity, binds Lhx3 is essentially the same way as Ldb1. The LIM domains from Lhx3 are shown as a grey surface. The Lhx3-binding domain from Isl1 is shown in green and the LIM-interaction domain from Ldb1 from the Lhx3-Ldb1 structure above is shown in gold.

A circular protein complex

[ PDB file ] [ PubMed link ]

We used intein technology to generate a circular protein complex between LMO4 and the LIM-binding domain of Ldb1 (Ldb1-LID). The proteins, which bind in a head-to-tail fashion are joined by a flexible linker at each end. The circular complex is more stable than a tethered complex where the C-terminus of LMO4 is linked to the N-terminus of Ldb1-LID, however, the crystal structure of this complex shows that the structures (in blue and gold), are identical. Curiously, when the order of a single tethering step is reversed (Ldb1-LID-to-LMO4) the resulting protein is just as stable as the circular complex.

Zinc finger 2 of ZNF265/ZRANB2

[ PDB file ]

The two zinc fingers of ZRANB2 (formerly known as ZNF265) can bind to single-stranded RNA with high sequence specificity. In addition to determining the structures of these two domains, we have used a combination of chemical shift mapping and mutagenesis to define the RNA-binding surface of these domains. Other zinc fingers in the same structural class (RanBP2-type zinc fingers) have been shown to mediate protein-protein interactions, another reminder of the versatility of small zinc-binding domains as recognition motifs.

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Lastest update: "Lab members page", on 24th Aug 2020.

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© W. Yung 2002