Zinc Transport

YiiP protein – structural basis for an alternating access model

Yiip is a zinc transporter and a member of the cation-diffusion facilitator family. Using the high-throughput instruments available at NYSBC to set and analyze 2D crystallization experiments, we have obtained helical crystals of YiiP from S. oneidensis. To reconstruct the 3D model of the crystal, two methods have been utilized: the Fourier-Bessel and the iterative helical real-space reconstruction techniques.  

A) 3D map of the tubular crystal. B) Isolated dimer and the fitting of our protein showing the inward-facing conformation (PDB 3J1Z). C) outward-facing conformation published by Lu et al., 2009 (PDB 3H90)

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Zinc Transport

YiiP protein – structural basis for an alternating access model

Micrograph of negatively stained YiiP? tubular crystals

Zinc homeostasis is crucial: zinc deficiency can affect several organs and excess zinc is highly toxic, resulting in cell death. Zinc is known to have an important role in several biological processes such as transcription or immune response, and in diseases like Alzheimer’s or type-2 diabetes. 

This work is the result of a collaborative effort between the labs of David Stokes, Iban Ubarretxena, Pawel Penczek, Marta Filizola and Ming Zhou, a part of TEMIMPS and was funded by a grant from the PSI.

A) 3D map of the tubular crystal. B) Isolated dimer and the fitting of our protein showing the inward-facing conformation (PDB 3J1Z). C) outward-facing conformation published by Lu et al., 2009 (PDB 3H90)

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Zinc Transport

Micrograph of negatively stained YiiP? tubular crystals

Zinc homeostasis is crucial: zinc deficiency can affect several organs and excess zinc is highly toxic, resulting in cell death. Zinc is known to have an important role in several biological processes such as transcription or immune response, and in diseases like Alzheimer’s or type-2 diabetes. 

Yiip is a zinc transporter and a member of the cation-diffusion facilitator family. Using the high-throughput instruments available at NYSBC to set and analyze 2D crystallization experiments, we have obtained helical crystals of YiiP^? from S. oneidensis. To reconstruct the 3D model of the crystal, two methods have been utilized: the Fourier-Bessel and the iterative helical real-space reconstruction techniques.   The X-Ray structure PDB 3H90 of YiiP^? from E. coli was used as a model for the manual docking and the molecular dynamics-based flexible fitting.  While the C-Terminal domain perfectly fits the higher radius densities of the map without any modification, the transmembrane domain displayed major conformational changes. The X-Ray structure, crystallized in the presence of zinc, shows an outward-facing conformation, while our structure, which sites are likely occupied by H+, shows the inward-facing conformation. It therefore appears that YiiP^? catalyzes the exchange of Zn2+ and of H+ across the membrane following the alternating access model described for several other transporters. 

This work is the result of a collaborative effort between the labs of David Stokes, Iban Ubarretxena, Pawel Penczek, Marta Filizola and Ming Zhou, a part of TEMIMPS and was funded by a grant from the PSI.

A) 3D map of the tubular crystal. B) Isolated dimer and the fitting of our protein showing the inward-facing conformation (PDB 3J1Z). C) outward-facing conformation published by Lu et al., 2009 (PDB 3H90)

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Zinc Transport

YiiP^? protein – structural basis for an alternating access model

Micrograph of negatively stained YiiP? tubular crystals

Zinc homeostasis is crucial: zinc deficiency can affect several organs and excess zinc is highly toxic, resulting in cell death. Zinc is known to have an important role in several biological processes such as transcription or immune response, and in diseases like Alzheimer’s or type-2 diabetes. 

Yiip is a zinc transporter and a member of the cation-diffusion facilitator family. Using the high-throughput instruments available at NYSBC to set and analyze 2D crystallization experiments, we have obtained helical crystals of YiiP^? from S. oneidensis. To reconstruct the 3D model of the crystal, two methods have been utilized: the Fourier-Bessel and the iterative helical real-space reconstruction techniques.   The X-Ray structure PDB 3H90 of YiiP^? from E. coli was used as a model for the manual docking and the molecular dynamics-based flexible fitting.  While the C-Terminal domain perfectly fits the higher radius densities of the map without any modification, the transmembrane domain displayed major conformational changes. The X-Ray structure, crystallized in the presence of zinc, shows an outward-facing conformation, while our structure, which sites are likely occupied by H+, shows the inward-facing conformation. It therefore appears that YiiP^? catalyzes the exchange of Zn2+ and of H+ across the membrane following the alternating access model described for several other transporters. 

This work is the result of a collaborative effort between the labs of David Stokes, Iban Ubarretxena, Pawel Penczek, Marta Filizola and Ming Zhou, a part of TEMIMPS and was funded by a grant from the PSI.

A) 3D map of the tubular crystal. B) Isolated dimer and the fitting of our protein showing the inward-facing conformation (PDB 3J1Z). C) outward-facing conformation published by Lu et al., 2009 (PDB 3H90)

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Zinc Transport

YiiP^? protein – structural basis for an alternating access model

Micrograph of negatively stained YiiP? tubular crystals

Zinc homeostasis is crucial: zinc deficiency can affect several organs and excess zinc is highly toxic, resulting in cell death. Zinc is known to have an important role in several biological processes such as transcription or immune response, and in diseases like Alzheimer’s or type-2 diabetes. 

Yiip is a zinc transporter and a member of the cation-diffusion facilitator family. Using the high-throughput instruments available at NYSBC to set and analyze 2D crystallization experiments, we have obtained helical crystals of YiiP^? from S. oneidensis. To reconstruct the 3D model of the crystal, two methods have been utilized: the Fourier-Bessel and the iterative helical real-space reconstruction techniques.   The X-Ray structure PDB 3H90 of YiiP^? from E. coli was used as a model for the manual docking and the molecular dynamics-based flexible fitting.  While the C-Terminal domain perfectly fits the higher radius densities of the map without any modification, the transmembrane domain displayed major conformational changes. The X-Ray structure, crystallized in the presence of zinc, shows an outward-facing conformation, while our structure, which sites are likely occupied by H+, shows the inward-facing conformation. It therefore appears that YiiP^? catalyzes the exchange of Zn2+ and of H+ across the membrane following the alternating access model described for several other transporters. 

This work is the result of a collaborative effort between the labs of David Stokes, Iban Ubarretxena, Pawel Penczek, Marta Filizola and Ming Zhou, a part of TEMIMPS and was funded by a grant from the PSI.

Zinc Transport

Zinc Transport

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