7php: Difference between revisions
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==Structure of Multidrug and Toxin Compound Extrusion (MATE) transporter NorM by NabFab-fiducial assisted cryo-EM== | |||
<StructureSection load='7php' size='340' side='right'caption='[[7php]], [[Resolution|resolution]] 3.47Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7php]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama], [https://en.wikipedia.org/wiki/Vibrio_cholerae_RC385 Vibrio cholerae RC385] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PHP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PHP 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]] 3.47Å</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=7php FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7php OCA], [https://pdbe.org/7php PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7php RCSB], [https://www.ebi.ac.uk/pdbsum/7php PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7php ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NORM_VIBCH NORM_VIBCH] Multidrug efflux pump that functions as a Na(+)/drug antiporter. Confers resistance to norfloxacin, ciprofloxacin, ofloxacin, daunomycin, doxorubicin, streptomycin, kanamycin, ethidium bromide and acriflavine.<ref>PMID:11583854</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
With conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody-target protein interaction. Here, we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon complementary-determining region grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryogenic electron microscopy (cryo-EM) structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of approximately 50 kDa. Using an additional anti-Fab nanobody further facilitated reliable initial three-dimensional structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, is humanized, and can be conveniently expressed in Escherichia coli in large amounts, it may be useful not only for structural biology but also for biomedical applications. | |||
Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins.,Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2115435118. doi: , 10.1073/pnas.2115435118. PMID:34782475<ref>PMID:34782475</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 7php" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Lama glama]] | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Vibrio cholerae RC385]] | |||
[[Category: Bloch JS]] | |||
[[Category: Kossiakoff AA]] | |||
[[Category: Kowal J]] | |||
[[Category: Locher KP]] | |||
[[Category: Mukherjee S]] | |||
[[Category: Niederer M]] | |||
[[Category: Pardon E]] | |||
[[Category: Steyaert J]] | |||
Latest revision as of 12:32, 9 October 2024
Structure of Multidrug and Toxin Compound Extrusion (MATE) transporter NorM by NabFab-fiducial assisted cryo-EMStructure of Multidrug and Toxin Compound Extrusion (MATE) transporter NorM by NabFab-fiducial assisted cryo-EM
Structural highlights
FunctionNORM_VIBCH Multidrug efflux pump that functions as a Na(+)/drug antiporter. Confers resistance to norfloxacin, ciprofloxacin, ofloxacin, daunomycin, doxorubicin, streptomycin, kanamycin, ethidium bromide and acriflavine.[1] Publication Abstract from PubMedWith conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody-target protein interaction. Here, we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon complementary-determining region grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryogenic electron microscopy (cryo-EM) structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of approximately 50 kDa. Using an additional anti-Fab nanobody further facilitated reliable initial three-dimensional structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, is humanized, and can be conveniently expressed in Escherichia coli in large amounts, it may be useful not only for structural biology but also for biomedical applications. Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins.,Bloch JS, Mukherjee S, Kowal J, Filippova EV, Niederer M, Pardon E, Steyaert J, Kossiakoff AA, Locher KP Proc Natl Acad Sci U S A. 2021 Nov 23;118(47):e2115435118. doi: , 10.1073/pnas.2115435118. PMID:34782475[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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