7kzx
From Proteopedia
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(New page: '''Unreleased structure''' The entry 7kzx is ON HOLD Authors: Description: Category: Unreleased Structures) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Cryo-EM structure of YiiP-Fab complex in Apo state== | |
| + | <StructureSection load='7kzx' size='340' side='right'caption='[[7kzx]], [[Resolution|resolution]] 4.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[7kzx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KZX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KZX FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4Å</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=7kzx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzx OCA], [https://pdbe.org/7kzx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kzx RCSB], [https://www.ebi.ac.uk/pdbsum/7kzx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzx ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/FIEF_SHEON FIEF_SHEON] Divalent metal cation transporter which exports Zn(2+), Cd(2+) and possibly Fe(2+) (PubMed:23341604, PubMed:29507252). Zn(2+)/H(+) antiporter capable of using the proton motive force to remove Zn(2+) from the cytoplasm (PubMed:34254979). May be involved in zinc and iron detoxification by efflux (By similarity).[UniProtKB:P69380]<ref>PMID:23341604</ref> <ref>PMID:29507252</ref> <ref>PMID:34254979</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | YiiP is a secondary transporter that couples Zn2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn2+. To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn2+ and validated its performance with known Zn2+-binding proteins. Using these tools, we find that, in the presence of Zn2+, YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn2+ binding sites and their role in the conformational dynamics that govern the transport cycle. | ||
| - | + | Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP.,Lopez-Redondo M, Fan S, Koide A, Koide S, Beckstein O, Stokes DL J Gen Physiol. 2021 Aug 2;153(8):e202112873. doi: 10.1085/jgp.202112873. Epub , 2021 Jul 13. PMID:34254979<ref>PMID:34254979</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| + | <div class="pdbe-citations 7kzx" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Antibody 3D structures|Antibody 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Shewanella oneidensis]] | ||
| + | [[Category: Beckstein O]] | ||
| + | [[Category: Fan S]] | ||
| + | [[Category: Koide A]] | ||
| + | [[Category: Koide S]] | ||
| + | [[Category: Lopez-Redondo ML]] | ||
| + | [[Category: Stokes DL]] | ||
Current revision
Cryo-EM structure of YiiP-Fab complex in Apo state
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