6gkd: Difference between revisions

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OCA

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-'''Unreleased structure'''
-The entry 6gkd is ON HOLD
+==human NBD1 of CFTR in complex with nanobodies D12 and G3a==
+<StructureSection load='6gkd' size='340' side='right'caption='[[6gkd]], [[Resolution|resolution]] 2.99&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6gkd]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GKD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.99&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PRD_900032:surcrose+isoform'>PRD_900032</scene>, <scene name='pdbligand=Z9N:(2S,3S,4S,5R)-2,5-bis(hydroxymethyl)oxolane-2,3,4-triol'>Z9N</scene></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=6gkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gkd OCA], [https://pdbe.org/6gkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gkd RCSB], [https://www.ebi.ac.uk/pdbsum/6gkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gkd ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/CFTR_HUMAN CFTR_HUMAN] Defects in CFTR are the cause of cystic fibrosis (CF) [MIM:[https://omim.org/entry/219700 219700]; also known as mucoviscidosis. CF is the most common genetic disease in the Caucasian population, with a prevalence of about 1 in 2'000 live births. Inheritance is autosomal recessive. CF is a common generalized disorder of exocrine gland function which impairs clearance of secretions in a variety of organs. It is characterized by the triad of chronic bronchopulmonary disease (with recurrent respiratory infections), pancreatic insufficiency (which leads to malabsorption and growth retardation) and elevated sweat electrolytes.<ref>PMID:1695717</ref> <ref>PMID:2236053</ref> <ref>PMID:1710600</ref> <ref>PMID:1284466</ref> <ref>PMID:1284468</ref> <ref>PMID:1284530</ref> <ref>PMID:1284529</ref> <ref>PMID:7680525</ref> <ref>PMID:7683628</ref> <ref>PMID:7683954</ref> <ref>PMID:7505694</ref> <ref>PMID:7504969</ref> <ref>PMID:7522211</ref> <ref>PMID:7513296</ref> <ref>PMID:7525450</ref> <ref>PMID:7520022</ref> <ref>PMID:7524913</ref> <ref>PMID:7524909</ref> <ref>PMID:7517264</ref> <ref>PMID:8081395</ref> <ref>PMID:7544319</ref> <ref>PMID:8522333</ref> <ref>PMID:7537150</ref> <ref>PMID:7541273</ref> <ref>PMID:7581407</ref> <ref>PMID:7543567</ref> <ref>PMID:7541510</ref> <ref>PMID:8800923</ref> <ref>PMID:8829633</ref> <ref>PMID:8723693</ref> <ref>PMID:8723695</ref> <ref>PMID:8956039</ref> <ref>PMID:9101301</ref> <ref>PMID:9222768</ref> <ref>PMID:9375855</ref> <ref>PMID:9401006</ref> <ref>PMID:9443874</ref> <ref>PMID:9521595</ref> <ref>PMID:9921909</ref> <ref>PMID:9736778</ref> <ref>PMID:9482579</ref> <ref>PMID:9554753</ref> <ref>PMID:9452048</ref> <ref>PMID:9452054</ref> <ref>PMID:9452073</ref> <ref>PMID:10094564</ref>   Defects in CFTR are the cause of congenital bilateral absence of the vas deferens (CBAVD) [MIM:[https://omim.org/entry/277180 277180]. CBAVD is an important cause of sterility in men and could represent an incomplete form of cystic fibrosis, as the majority of men suffering from cystic fibrosis lack the vas deferens.<ref>PMID:7529962</ref> <ref>PMID:7539342</ref> <ref>PMID:9067761</ref> <ref>PMID:10651488</ref> [:]
+== Function ==
+[https://www.uniprot.org/uniprot/CFTR_HUMAN CFTR_HUMAN] Involved in the transport of chloride ions. May regulate bicarbonate secretion and salvage in epithelial cells by regulating the SLC4A7 transporter. Can inhibit the chloride channel activity of ANO1.<ref>PMID:22178883</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The leading cause of cystic fibrosis (CF) is the deletion of phenylalanine 508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR). The mutation affects the thermodynamic stability of the domain and the integrity of the interface between NBD1 and the transmembrane domain leading to its clearance by the quality control system. Here, we develop nanobodies targeting NBD1 of human CFTR and demonstrate their ability to stabilize both isolated NBD1 and full-length protein. Crystal structures of NBD1-nanobody complexes provide an atomic description of the epitopes and reveal the molecular basis for stabilization. Furthermore, our data uncover a conformation of CFTR, involving detachment of NBD1 from the transmembrane domain, which contrast with the compact assembly observed in cryo-EM structures. This unexpected interface rearrangement is likely to have major relevance for CF pathogenesis but also for the normal function of CFTR and other ABC proteins.
-Authors: Sigoillot, M., Overtus, M., Grodecka, M., Scholl, D., Garcia-Pino, A., Laeremans, T., He, L., Pardon, E., Hildebrandt, E., Urbatsch, I., Steyaert, J., Riordan, J.R., Govaerts, C.
+Domain-interface dynamics of CFTR revealed by stabilizing nanobodies.,Sigoillot M, Overtus M, Grodecka M, Scholl D, Garcia-Pino A, Laeremans T, He L, Pardon E, Hildebrandt E, Urbatsch I, Steyaert J, Riordan JR, Govaerts C Nat Commun. 2019 Jun 14;10(1):2636. doi: 10.1038/s41467-019-10714-y. PMID:31201318<ref>PMID:31201318</ref>
-Description: human NBD1 of CFTR in complex with nanobodies D12 and G3a
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Steyaert, J]]
+<div class="pdbe-citations 6gkd" style="background-color:#fffaf0;"></div>
-[[Category: Garcia-Pino, A]]
-[[Category: Govaerts, C]]
+==See Also==
-[[Category: Overtus, M]]
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
-[[Category: Laeremans, T]]
+== References ==
-[[Category: Urbatsch, I]]
+<references/>
-[[Category: Sigoillot, M]]
+__TOC__
-[[Category: Grodecka, M]]
+</StructureSection>
-[[Category: Pardon, E]]
+[[Category: Homo sapiens]]
-[[Category: He, L]]
+[[Category: Lama glama]]
-[[Category: Riordan, J.R]]
+[[Category: Large Structures]]
-[[Category: Hildebrandt, E]]
+[[Category: Garcia-Pino A]]
-[[Category: Scholl, D]]
+[[Category: Govaerts C]]
+[[Category: Grodecka M]]
+[[Category: He L]]
+[[Category: Hildebrandt E]]
+[[Category: Laeremans T]]
+[[Category: Overtus M]]
+[[Category: Pardon E]]
+[[Category: Riordan JR]]
+[[Category: Scholl D]]
+[[Category: Sigoillot M]]
+[[Category: Steyaert J]]
+[[Category: Urbatsch I]]