Structural basis for the Smad5 MH1 domain to recognize different DNA sequences.
Structural basis for the Smad5 MH1 domain to recognize different DNA sequences.
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DOI：
10.1093/nar/gkx226
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发表时间：
2017-06-02
影响因子：
14.9
通讯作者：
Wu JW
中科院分区：
文献类型：
--
作者：
Chai N;Li WX;Wang J;Wang ZX;Yang SM;Wu JW
Smad5-MH1/GC-BRE晶体结构的空间群先前被指定为P31。然而，在重新检查晶体学数据之后，我们希望将空间群修正为更高对称性的P6422。由于GC-BRE DNA的序列是回文的，因此修改后的结构包含一个Smad5-MH1单体和一个不对称单元中的单个GC-BRE DNA链，其中14个有序核苷酸与对称相关的DNA链形成双螺旋。两个Smad5-MH1单体和一个GC-BRE DNA双链的生理复合物（2:1 Smad5-MH1/GC-BRE复合物）与先前的P31空间群Smad-DNA复合物基本相同，180个对齐残基的C RMSD为0.4 a。由于分辨率有限，并非所有的侧链都能以高置信度放置，一些残基的侧链被去除。幸运的是，参与蛋白质-DNA相互作用的残基大多是有序的，两个Smad5-MH1单体与GC-BRE DNA双链的相互作用模式是不变的。由于该结构的空间群发生了变化，我们对图3（重新标记分子和侧链）和补充图S3（替换面板A和B）进行了修改。
The space group for the crystal structure of Smad5-MH1/GC-BRE was previously assigned as P31. After re-examining the crystallographic data, however, we wish to revise the space group to a higher symmetry one, P6422. As the sequence of GC-BRE DNA is palindromic, the revised structure contains one Smad5-MH1 monomer and a single GC-BRE DNA strand in an asymmetric unit, where the 14 ordered nucleotides form a double helix with a symmetry-related DNA strand. The physiological complex of two Smad5-MH1 monomers and one GC-BRE DNA duplex (the 2: 1 Smad5-MH1/GC-BRE complex) is basically the same as the previous Smad-DNA complex of P31 space group, with a C RMSD of∼ 0.4 A for 180 aligning residues.Owing to the limited resolution, not all side chains could be placed with high confidence and the side chains of some residues were removed. Fortunately, residues involved in the protein-DNA interactions are mostly ordered, and the interaction mode of two Smad5-MH1 monomers with the GC-BRE DNA duplex is unchanged. As the space group of this structure is changed, we revise Figure 3 (relabeling the molecules and side chains) and Supplementary Figure S3 (replacing panels A and B).