5jdq

From Proteopedia

(Difference between revisions)

Current revision

Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 100 mM Na+ and 10mM Sr2+

Structural highlights

5jdq is a 1 chain structure with sequence from Methanocaldococcus jannaschii DSM 2661. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Y091_METJA

Publication Abstract from PubMed

Na+/Ca2+ exchangers use the Na+ electrochemical gradient across the plasma membrane to extrude intracellular Ca2+ and play a central role in Ca2+ homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na+, Ca2+ or Sr2+ in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3:1 Na+/Ca2+-exchange stoichiometry and reveals the conformational changes at the onset of the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. These calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion occupancy, thereby explaining the emergence of strictly coupled Na+/Ca2+ antiport.

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.,Liao J, Marinelli F, Lee C, Huang Y, Faraldo-Gomez JD, Jiang Y Nat Struct Mol Biol. 2016 May 16. doi: 10.1038/nsmb.3230. PMID:27183196^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Liao J, Marinelli F, Lee C, Huang Y, Faraldo-Gomez JD, Jiang Y. Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger. Nat Struct Mol Biol. 2016 May 16. doi: 10.1038/nsmb.3230. PMID:27183196 doi:http://dx.doi.org/10.1038/nsmb.3230

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jdq"

Categories: Large Structures | Methanocaldococcus jannaschii DSM 2661 | Faraldo-Gomez JD | Jiang YX | Liao J

@@ Line 3: / Line 3: @@
 <StructureSection load='5jdq' size='340' side='right'caption='[[5jdq]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jdq]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metja Metja]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JDQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jdq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JDQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5jdn|5jdn]], [[5jdm|5jdm]], [[5jdl|5jdl]], [[5jdh|5jdh]], [[5jdg|5jdg]], [[5jdf|5jdf]], [[5hwx|5hwx]], [[5hwy|5hwy]], [[5hxc|5hxc]], [[5hxe|5hxe]], [[5hxh|5hxh]], [[5hxr|5hxr]], [[5hxs|5hxs]], [[5hya|5hya]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0091 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243232 METJA])</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=5jdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdq OCA], [https://pdbe.org/5jdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jdq RCSB], [https://www.ebi.ac.uk/pdbsum/5jdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdq ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5jdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jdq OCA], [http://pdbe.org/5jdq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jdq RCSB], [http://www.ebi.ac.uk/pdbsum/5jdq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jdq ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Y091_METJA Y091_METJA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5jdq" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Sodium-calcium exchanger|Sodium-calcium exchanger]]
 == References ==
 <references/>
@@ Line 26: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Metja]]
+[[Category: Methanocaldococcus jannaschii DSM 2661]]
-[[Category: Faraldo-Gomez, J D]]
+[[Category: Faraldo-Gomez JD]]
-[[Category: Jiang, Y X]]
+[[Category: Jiang YX]]
-[[Category: Liao, J]]
+[[Category: Liao J]]
-[[Category: Calcium signalling]]
-[[Category: Induced conformational change]]
-[[Category: Membrane protein]]
-[[Category: Membrane transporter]]
-[[Category: Na+/ca2+ exchange]]

5jdq

From Proteopedia

Current revision

Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 100 mM Na+ and 10mM Sr2+

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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