7phq: Difference between revisions
New page: '''Unreleased structure''' The entry 7phq is ON HOLD Authors: Description: Category: Unreleased Structures |
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==Structure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EM== | |||
<StructureSection load='7phq' size='340' side='right'caption='[[7phq]], [[Resolution|resolution]] 8.45Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7phq]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama], [https://en.wikipedia.org/wiki/Staphylococcus_capitis Staphylococcus capitis] 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=7PHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PHQ 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]] 8.45Å</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=7phq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7phq OCA], [https://pdbe.org/7phq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7phq RCSB], [https://www.ebi.ac.uk/pdbsum/7phq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7phq ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A4U9TNH6_STACP A0A4U9TNH6_STACP] H(+)-stimulated, divalent metal cation uptake system.[HAMAP-Rule:MF_00221] | |||
<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 7phq" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Lama glama]] | |||
[[Category: Large Structures]] | |||
[[Category: Staphylococcus capitis]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Bloch JS]] | |||
[[Category: Kossiakoff AA]] | |||
[[Category: Kowal J]] | |||
[[Category: Locher KP]] | |||
[[Category: Mukherjee S]] | |||
Latest revision as of 09:40, 21 November 2024
Structure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EMStructure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EM
Structural highlights
FunctionA0A4U9TNH6_STACP H(+)-stimulated, divalent metal cation uptake system.[HAMAP-Rule:MF_00221] 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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