3ich

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of cyclophilin B at 1.2 A resolution

Structural highlights

3ich is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PPIB_HUMAN Defects in PPIB are the cause of osteogenesis imperfecta type 9 (OI9) [MIM:259440. OI9 is a connective tissue disorder characterized by bone fragility, low bone mass and bowing of limbs due to multiple fractures. Short limb dwarfism and blue sclerae are observed in some but not all patients.^[1] ^[2]

Function

PPIB_HUMAN PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Little is known about how chaperones in the endoplasmic reticulum are organized into complexes to assist in the proper folding of secreted proteins. One notable exception is the complex of ERp57 and calnexin that functions as part the calnexin cycle to direct disulfide bond formation in N-glycoproteins. Here, we report three new complexes composed of the peptidyl prolyl cis-trans isomerase cyclophilin B and any of the lectin chaperones: calnexin (CNX), calreticulin (CRT), or calmegin (CMG). The 1.7 A crystal structure of cyclophilin with the proline-rich P-domain of CMG reveals that binding is mediated by the same surface that binds ERp57. We use NMR titrations and mutagenesis to measure low micromolar binding of cyclophilin to all three lectin chaperones and identify essential interfacial residues. The immunosuppressant cyclosporin A did not affect complex formation, confirming the functional independence of the P-domain-binding and proline isomerization sites of cyclophilin. Our results reveal the P-domain functions as a unique protein-protein interaction domain and implicate a peptidyl prolyl isomerase as a new element in the calnexin cycle.

Structural basis of cyclophilin B binding by the calnexin/calreticulin P-domain.,Kozlov G, Bastos-Aristizabal S, Maattanen P, Rosenauer A, Zheng F, Killikelly A, Trempe JF, Thomas DY, Gehring K J Biol Chem. 2010 Sep 3. PMID:20801878^[3]

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

References

↑ van Dijk FS, Nesbitt IM, Zwikstra EH, Nikkels PG, Piersma SR, Fratantoni SA, Jimenez CR, Huizer M, Morsman AC, Cobben JM, van Roij MH, Elting MW, Verbeke JI, Wijnaendts LC, Shaw NJ, Hogler W, McKeown C, Sistermans EA, Dalton A, Meijers-Heijboer H, Pals G. PPIB mutations cause severe osteogenesis imperfecta. Am J Hum Genet. 2009 Oct;85(4):521-7. doi: 10.1016/j.ajhg.2009.09.001. Epub 2009 , Sep 24. PMID:19781681 doi:10.1016/j.ajhg.2009.09.001
↑ Barnes AM, Carter EM, Cabral WA, Weis M, Chang W, Makareeva E, Leikin S, Rotimi CN, Eyre DR, Raggio CL, Marini JC. Lack of cyclophilin B in osteogenesis imperfecta with normal collagen folding. N Engl J Med. 2010 Feb 11;362(6):521-8. doi: 10.1056/NEJMoa0907705. Epub 2010 Jan, 20. PMID:20089953 doi:10.1056/NEJMoa0907705
↑ Kozlov G, Bastos-Aristizabal S, Maattanen P, Rosenauer A, Zheng F, Killikelly A, Trempe JF, Thomas DY, Gehring K. Structural basis of cyclophilin B binding by the calnexin/calreticulin P-domain. J Biol Chem. 2010 Sep 3. PMID:20801878 doi:10.1074/jbc.M110.160101

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ich"

Categories: Homo sapiens | Large Structures | Gehring K | Kozlov G

@@ Line 1: / Line 1: @@
-[[Image:3ich.png|left|200px]]
-<!--
+==Crystal structure of cyclophilin B at 1.2 A resolution==
-The line below this paragraph, containing "STRUCTURE_3ich", creates the "Structure Box" on the page.
+<StructureSection load='3ich' size='340' side='right'caption='[[3ich]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3ich]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ICH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ICH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</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=3ich FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ich OCA], [https://pdbe.org/3ich PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ich RCSB], [https://www.ebi.ac.uk/pdbsum/3ich PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ich ProSAT]</span></td></tr>
-{{STRUCTURE_3ich|  PDB=3ich  |  SCENE=  }}
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PPIB_HUMAN PPIB_HUMAN] Defects in PPIB are the cause of osteogenesis imperfecta type 9 (OI9) [MIM:[https://omim.org/entry/259440 259440]. OI9 is a connective tissue disorder characterized by bone fragility, low bone mass and bowing of limbs due to multiple fractures. Short limb dwarfism and blue sclerae are observed in some but not all patients.<ref>PMID:19781681</ref> <ref>PMID:20089953</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PPIB_HUMAN PPIB_HUMAN] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
+== 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/ic/3ich_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=3ich ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Little is known about how chaperones in the endoplasmic reticulum are organized into complexes to assist in the proper folding of secreted proteins. One notable exception is the complex of ERp57 and calnexin that functions as part the calnexin cycle to direct disulfide bond formation in N-glycoproteins. Here, we report three new complexes composed of the peptidyl prolyl cis-trans isomerase cyclophilin B and any of the lectin chaperones: calnexin (CNX), calreticulin (CRT), or calmegin (CMG). The 1.7 A crystal structure of cyclophilin with the proline-rich P-domain of CMG reveals that binding is mediated by the same surface that binds ERp57. We use NMR titrations and mutagenesis to measure low micromolar binding of cyclophilin to all three lectin chaperones and identify essential interfacial residues. The immunosuppressant cyclosporin A did not affect complex formation, confirming the functional independence of the P-domain-binding and proline isomerization sites of cyclophilin. Our results reveal the P-domain functions as a unique protein-protein interaction domain and implicate a peptidyl prolyl isomerase as a new element in the calnexin cycle.
-===Crystal structure of cyclophilin B at 1.2 A resolution===
+Structural basis of cyclophilin B binding by the calnexin/calreticulin P-domain.,Kozlov G, Bastos-Aristizabal S, Maattanen P, Rosenauer A, Zheng F, Killikelly A, Trempe JF, Thomas DY, Gehring K J Biol Chem. 2010 Sep 3. PMID:20801878<ref>PMID:20801878</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20801878}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3ich" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20801878 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_20801878}}
-==About this Structure==
-[[3ich]] is a 1 chain structure of [[Cyclophilin]] 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=3ICH OCA].
 ==See Also==
-*[[Cyclophilin]]
+*[[Cyclophilin 3D structures|Cyclophilin 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:20801878</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Peptidylprolyl isomerase]]
+[[Category: Large Structures]]
-[[Category: Gehring, K.]]
+[[Category: Gehring K]]
-[[Category: Kozlov, G.]]
+[[Category: Kozlov G]]
-[[Category: Beta sandwich]]
-[[Category: Cyclosporin]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Glycoprotein]]
-[[Category: Isomerase]]
-[[Category: Rotamase]]

3ich

From Proteopedia

Current revision

Crystal structure of cyclophilin B at 1.2 A resolution

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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