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.

5tal

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 09:02, 18 July 2018

Warning: this is a large structure, and loading might take a long time or not happen at all.

Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 1&2)

Structural highlights

5tal is a 8 chain structure with sequence from Human and Oryctolagus cuniculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
NonStd Res:
Related:	5t15, 5t9m, 5t9n, 5t9r, 5t9s, 5t9v, 5ta3, 5tam, 5tan, 5taq, 5tap, 5tas, 5tat, 5tau, 5tav, 5taw, 5tax, 5tay, 5taz, 5tb0, 5tb1, 5tb2, 5tb3, 5tb4
Gene:	FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 (HUMAN)
Activity:	Peptidylprolyl isomerase, with EC number 5.2.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Warning: this is a large structure, and loading might take a long time or not happen at all.

Function

[RYR1_RABIT] Calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. Repeated very high-level exercise increases the open probability of the channel and leads to Ca(2+) leaking into the cytoplasm. Can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. Required for normal embryonic development of muscle fibers and skeletal muscle. Required for normal heart morphogenesis, skin development and ossification during embryogenesis (By similarity).^[1] ^[2] [FKB1B_HUMAN] Has the potential to contribute to the immunosuppressive and toxic effects of FK506 and rapamycin. PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Publication Abstract from PubMed

The type-1 ryanodine receptor (RyR1) is an intracellular calcium (Ca(2+)) release channel required for skeletal muscle contraction. Here, we present cryo-EM reconstructions of RyR1 in multiple functional states revealing the structural basis of channel gating and ligand-dependent activation. Binding sites for the channel activators Ca(2+), ATP, and caffeine were identified at interdomain interfaces of the C-terminal domain. Either ATP or Ca(2+) alone induces conformational changes in the cytoplasmic assembly ("priming"), without pore dilation. In contrast, in the presence of all three activating ligands, high-resolution reconstructions of open and closed states of RyR1 were obtained from the same sample, enabling analyses of conformational changes associated with gating. Gating involves global conformational changes in the cytosolic assembly accompanied by local changes in the transmembrane domain, which include bending of the S6 transmembrane segment and consequent pore dilation, displacement, and deformation of the S4-S5 linker and conformational changes in the pseudo-voltage-sensor domain.

Structural Basis for Gating and Activation of RyR1.,des Georges A, Clarke OB, Zalk R, Yuan Q, Condon KJ, Grassucci RA, Hendrickson WA, Marks AR, Frank J Cell. 2016 Sep 22;167(1):145-157.e17. doi: 10.1016/j.cell.2016.08.075. PMID:27662087^[3]

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

References

↑ Dulhunty AF, Laver DR, Gallant EM, Casarotto MG, Pace SM, Curtis S. Activation and inhibition of skeletal RyR channels by a part of the skeletal DHPR II-III loop: effects of DHPR Ser687 and FKBP12. Biophys J. 1999 Jul;77(1):189-203. PMID:10388749 doi:10.1016/S0006-3495(99)76881-5
↑ Kakizawa S, Yamazawa T, Chen Y, Ito A, Murayama T, Oyamada H, Kurebayashi N, Sato O, Watanabe M, Mori N, Oguchi K, Sakurai T, Takeshima H, Saito N, Iino M. Nitric oxide-induced calcium release via ryanodine receptors regulates neuronal function. EMBO J. 2011 Oct 28;31(2):417-28. doi: 10.1038/emboj.2011.386. PMID:22036948 doi:10.1038/emboj.2011.386
↑ des Georges A, Clarke OB, Zalk R, Yuan Q, Condon KJ, Grassucci RA, Hendrickson WA, Marks AR, Frank J. Structural Basis for Gating and Activation of RyR1. Cell. 2016 Sep 22;167(1):145-157.e17. doi: 10.1016/j.cell.2016.08.075. PMID:27662087 doi:http://dx.doi.org/10.1016/j.cell.2016.08.075

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 3: / Line 3: @@
 <StructureSection load='5tal' size='340' side='right' caption='[[5tal]], [[Resolution|resolution]] 4.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5tal]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TAL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TAL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5tal]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TAL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TAL FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5t15|5t15]], [[5t9m|5t9m]], [[5t9n|5t9n]], [[5t9r|5t9r]], [[5t9s|5t9s]], [[5t9v|5t9v]], [[5ta3|5ta3]], [[5tam|5tam]], [[5tan|5tan]], [[5taq|5taq]], [[5tap|5tap]], [[5tas|5tas]], [[5tat|5tat]], [[5tau|5tau]], [[5tav|5tav]], [[5taw|5taw]], [[5tax|5tax]], [[5tay|5tay]], [[5taz|5taz]], [[5tb0|5tb0]], [[5tb1|5tb1]], [[5tb2|5tb2]], [[5tb3|5tb3]], [[5tb4|5tb4]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=5tal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tal OCA], [http://pdbe.org/5tal PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tal RCSB], [http://www.ebi.ac.uk/pdbsum/5tal PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tal ProSAT]</span></td></tr>
@@ Line 22: / Line 23: @@
 </div>
 <div class="pdbe-citations 5tal" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ryanodine receptor|Ryanodine receptor]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
 [[Category: Oryctolagus cuniculus]]
 [[Category: Peptidylprolyl isomerase]]

5tal

From Proteopedia

Revision as of 09:02, 18 July 2018

Structure of rabbit RyR1 (Caffeine/ATP/Ca2+ dataset, class 1&2)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox