This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2agv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:17, 25 October 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2agv.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of the SR CA2+-ATPASE with BHQ and TG==
-
|PDB= 2agv |SIZE=350|CAPTION= <scene name='initialview01'>2agv</scene>, resolution 2.40&Aring;
+
<StructureSection load='2agv' size='340' side='right'caption='[[2agv]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TG1:OCTANOIC+ACID+[3S-[3ALPHA,+3ABETA,+4ALPHA,+6BETA,+6ABETA,+7BETA,+8ALPHA(Z),+9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL+ESTER'>TG1</scene>, <scene name='pdbligand=BHQ:2,5-DITERT-BUTYLBENZENE-1,4-DIOL'>BHQ</scene> and <scene name='pdbligand=PTY:PHOSPHATIDYLETHANOLAMINE'>PTY</scene>
+
<table><tr><td colspan='2'>[[2agv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AGV FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Calcium-transporting_ATPase Calcium-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.8 3.6.3.8]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BHQ:2,5-DITERT-BUTYLBENZENE-1,4-DIOL'>BHQ</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PTY:PHOSPHATIDYLETHANOLAMINE'>PTY</scene>, <scene name='pdbligand=TG1:OCTANOIC+ACID+[3S-[3ALPHA,+3ABETA,+4ALPHA,+6BETA,+6ABETA,+7BETA,+8ALPHA(Z),+9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX+Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL+ESTER'>TG1</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=2agv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2agv OCA], [https://pdbe.org/2agv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2agv RCSB], [https://www.ebi.ac.uk/pdbsum/2agv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2agv ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AT2A1_RABIT AT2A1_RABIT] This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen. Contributes to calcium sequestration involved in muscular excitation/contraction (By similarity).
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ag/2agv_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2agv ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but also a H(+) pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-A-resolution crystal structure of the Ca(2+)-ATPase in the absence of Ca(2+) stabilized by two inhibitors, dibutyldihydroxybenzene, which bridges two transmembrane helices, and thapsigargin, also bound in the membrane region. Now visualized are water and several phospholipid molecules, one of which occupies a cleft between two transmembrane helices. Atomic models of the Ca(2+) binding sites with explicit hydrogens derived by continuum electrostatic calculations show how water and protons fill the space and compensate charge imbalance created by Ca(2+)-release. They suggest that H(+) countertransport is a consequence of a requirement for maintaining structural integrity of the empty Ca(2+)-binding sites. For this reason, cation countertransport is probably mandatory for all P-type ATPases and possibly accompanies transport of water as well.
-
'''Crystal structure of the SR CA2+-ATPASE with BHQ and TG'''
+
Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+).,Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, Toyoshima C Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14489-96. Epub 2005 Sep 6. PMID:16150713<ref>PMID:16150713</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2agv" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but also a H(+) pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-A-resolution crystal structure of the Ca(2+)-ATPase in the absence of Ca(2+) stabilized by two inhibitors, dibutyldihydroxybenzene, which bridges two transmembrane helices, and thapsigargin, also bound in the membrane region. Now visualized are water and several phospholipid molecules, one of which occupies a cleft between two transmembrane helices. Atomic models of the Ca(2+) binding sites with explicit hydrogens derived by continuum electrostatic calculations show how water and protons fill the space and compensate charge imbalance created by Ca(2+)-release. They suggest that H(+) countertransport is a consequence of a requirement for maintaining structural integrity of the empty Ca(2+)-binding sites. For this reason, cation countertransport is probably mandatory for all P-type ATPases and possibly accompanies transport of water as well.
+
*[[ATPase 3D structures|ATPase 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
2AGV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AGV OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
[[Category: Large Structures]]
-
Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)., Obara K, Miyashita N, Xu C, Toyoshima I, Sugita Y, Inesi G, Toyoshima C, Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14489-96. Epub 2005 Sep 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16150713 16150713]
+
-
[[Category: Calcium-transporting ATPase]]
+
[[Category: Oryctolagus cuniculus]]
[[Category: Oryctolagus cuniculus]]
-
[[Category: Single protein]]
+
[[Category: Norimatsu Y]]
-
[[Category: Norimatsu, Y.]]
+
[[Category: Obara K]]
-
[[Category: Obara, K.]]
+
[[Category: Toyoshima C]]
-
[[Category: Toyoshima, C.]]
+
-
[[Category: BHQ]]
+
-
[[Category: NA]]
+
-
[[Category: PTY]]
+
-
[[Category: TG1]]
+
-
[[Category: had fold]]
+
-
[[Category: membrane protein]]
+
-
[[Category: p-type atpase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:49:30 2008''
+

Current revision

Crystal structure of the SR CA2+-ATPASE with BHQ and TG

PDB ID 2agv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2agv"
Personal tools