2pm7

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine version

Structural highlights

2pm7 is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.35Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SEC31_YEAST Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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

COPII-coated vesicles export newly synthesized proteins from the endoplasmic reticulum. The COPII coat consists of the Sec23/24-Sar1 complex that selects cargo and the Sec13/31 assembly unit that can polymerize into an octahedral cage and deform the membrane into a bud. Crystallographic analysis of the assembly unit reveals a 28 nm long rod comprising a central alpha-solenoid dimer capped by two beta-propeller domains at each end. We construct a molecular model of the COPII cage by fitting Sec13/31 crystal structures into a recently determined electron microscopy density map. The vertex geometry involves four copies of the Sec31 beta-propeller that converge through their axial ends; there is no interdigitation of assembly units of the kind seen in clathrin cages. We also propose that the assembly unit has a central hinge-an arrangement of interlocked alpha-solenoids-about which it can bend to adapt to cages of variable curvature.

Structure and organization of coat proteins in the COPII cage.,Fath S, Mancias JD, Bi X, Goldberg J Cell. 2007 Jun 29;129(7):1325-36. PMID:17604721^[7]

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

References

↑ Bednarek SY, Ravazzola M, Hosobuchi M, Amherdt M, Perrelet A, Schekman R, Orci L. COPI- and COPII-coated vesicles bud directly from the endoplasmic reticulum in yeast. Cell. 1995 Dec 29;83(7):1183-96. PMID:8548805
↑ Wuestehube LJ, Duden R, Eun A, Hamamoto S, Korn P, Ram R, Schekman R. New mutants of Saccharomyces cerevisiae affected in the transport of proteins from the endoplasmic reticulum to the Golgi complex. Genetics. 1996 Feb;142(2):393-406. PMID:8852839
↑ Salama NR, Chuang JS, Schekman RW. Sec31 encodes an essential component of the COPII coat required for transport vesicle budding from the endoplasmic reticulum. Mol Biol Cell. 1997 Feb;8(2):205-17. PMID:9190202
↑ Campbell JL, Schekman R. Selective packaging of cargo molecules into endoplasmic reticulum-derived COPII vesicles. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):837-42. PMID:9023343
↑ Matsuoka K, Schekman R. The use of liposomes to study COPII- and COPI-coated vesicle formation and membrane protein sorting. Methods. 2000 Apr;20(4):417-28. PMID:10720463 doi:10.1006/meth.2000.0955
↑ Sato K, Nakano A. Reconstitution of coat protein complex II (COPII) vesicle formation from cargo-reconstituted proteoliposomes reveals the potential role of GTP hydrolysis by Sar1p in protein sorting. J Biol Chem. 2004 Jan 9;279(2):1330-5. Epub 2003 Nov 19. PMID:14627716 doi:10.1074/jbc.C300457200
↑ Fath S, Mancias JD, Bi X, Goldberg J. Structure and organization of coat proteins in the COPII cage. Cell. 2007 Jun 29;129(7):1325-36. PMID:17604721 doi:10.1016/j.cell.2007.05.036

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pm7"

@@ Line 1: / Line 1: @@
 ==Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine version==
-<StructureSection load='2pm7' size='340' side='right' caption='[[2pm7]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+<StructureSection load='2pm7' size='340' side='right'caption='[[2pm7]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pm7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PM7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PM7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pm7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PM7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PM7 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 2.35&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2pm6|2pm6]], [[2pm9|2pm9]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">WEB1, SEC31 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), SEC13, ANU3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2pm7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pm7 OCA], [https://pdbe.org/2pm7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pm7 RCSB], [https://www.ebi.ac.uk/pdbsum/2pm7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pm7 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pm7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pm7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pm7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pm7 PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/SEC31_YEAST SEC31_YEAST] Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules.<ref>PMID:8548805</ref> <ref>PMID:8852839</ref> <ref>PMID:9190202</ref> <ref>PMID:9023343</ref> <ref>PMID:10720463</ref> <ref>PMID:14627716</ref>
 == 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/pm/2pm7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pm/2pm7_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2pm7 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2pm7" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Bi, X.]]
+[[Category: Bi X]]
-[[Category: Fath, S.]]
+[[Category: Fath S]]
-[[Category: Goldberg, J.]]
+[[Category: Goldberg J]]
-[[Category: Mancias, J D.]]
+[[Category: Mancias JD]]
-[[Category: Alpha solenoid]]
-[[Category: Beta propeller]]
-[[Category: Protein transport]]

2pm7

From Proteopedia

Current revision

Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat, selenomethionine version

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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