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.

3qyu

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 10:02, 5 August 2016

Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature

Structural highlights

3qyu is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	3qyw, 3qyz
Gene:	PPIF, CYP3 (HUMAN)
Activity:	Peptidylprolyl isomerase, with EC number 5.2.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PPIF_HUMAN] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.^[1] ^[2]

Publication Abstract from PubMed

X-ray crystallography is now a recognized technique for ligand screening, especially for fragment-based drug design. However, protein crystal handling is still tedious and limits further automation. An alternative method for the solution of crystal structures of proteins in complex with small ligands is proposed. Crystallization drops are directly exposed to an X-ray beam after cocrystallization or soaking with the desired ligands. The use of dedicated plates in connection with an optimal parametrization of the G-rob robot allows efficient data collection. Three proteins currently under study in our laboratory for ligand screening by X-ray crystallography were used as validation test cases. The protein crystals belonged to different space groups, including a challenging monoclinic case. The resulting diffraction data can lead to clear ligand recognition, including indication of alternating conformations. These results demonstrate a possible method for automation of ligand screening by X-ray crystallography.

In-plate protein crystallization, in situ ligand soaking and X-ray diffraction.,le Maire A, Gelin M, Pochet S, Hoh F, Pirocchi M, Guichou JF, Ferrer JL, Labesse G Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):747-55. doi:, 10.1107/S0907444911023249. Epub 2011 Aug 9. PMID:21904027^[3]

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

References

↑ Eliseev RA, Malecki J, Lester T, Zhang Y, Humphrey J, Gunter TE. Cyclophilin D interacts with Bcl2 and exerts an anti-apoptotic effect. J Biol Chem. 2009 Apr 10;284(15):9692-9. doi: 10.1074/jbc.M808750200. Epub 2009, Feb 19. PMID:19228691 doi:http://dx.doi.org/10.1074/jbc.M808750200
↑ Vaseva AV, Marchenko ND, Ji K, Tsirka SE, Holzmann S, Moll UM. p53 opens the mitochondrial permeability transition pore to trigger necrosis. Cell. 2012 Jun 22;149(7):1536-48. doi: 10.1016/j.cell.2012.05.014. PMID:22726440 doi:10.1016/j.cell.2012.05.014
↑ le Maire A, Gelin M, Pochet S, Hoh F, Pirocchi M, Guichou JF, Ferrer JL, Labesse G. In-plate protein crystallization, in situ ligand soaking and X-ray diffraction. Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):747-55. doi:, 10.1107/S0907444911023249. Epub 2011 Aug 9. PMID:21904027 doi:10.1107/S0907444911023249

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/3qyu"

@@ Line 1: / Line 1: @@
 ==Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature==
 <StructureSection load='3qyu' size='340' side='right' caption='[[3qyu]], [[Resolution|resolution]] 1.54&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3qyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3qyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QYU FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qyw|3qyw]], [[3qyz|3qyz]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([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=3qyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3qyu RCSB], [http://www.ebi.ac.uk/pdbsum/3qyu PDBsum]</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=3qyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qyu OCA], [http://pdbe.org/3qyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qyu RCSB], [http://www.ebi.ac.uk/pdbsum/3qyu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qyu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3qyu" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 25: / Line 27: @@
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
 [[Category: Peptidylprolyl isomerase]]
 [[Category: Colliandre, L]]

3qyu

From Proteopedia

Revision as of 10:02, 5 August 2016

Crystal structure of human cyclophilin D at 1.54 A resolution at room temperature

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