3e5h: Difference between revisions

Latest revision as of 12:58, 30 August 2023

Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form

Structural highlights

3e5h is a 1 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 2hy4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.499Å
Ligands:	GNP, GOL, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

RAB28_HUMAN Cone rod dystrophy. The disease is caused by mutations affecting the gene represented in this entry.^[1]

Function

RAB28_HUMAN

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

Rab GTPases are essential regulators of membrane trafficking. We report crystal structures of Rab28 in the active (GppNHp-bound) and inactive (GDP-3'P-bound) forms at 1.5 and 1.1A resolution. Rab28 is a distant member of the Rab family. While the overall fold of Rab28 resembles that of other Rab GTPases, it undergoes a larger nucleotide-dependent conformational change than other members of this family. Added flexibility resulting from a double-glycine motif at the beginning of switch 2 might partially account for this observation. The double-glycine motif, which is conserved in the Arf family, only occurs in Rab28 and Rab7B of the Rab family, and may have a profound effect on their catalytic activities.

Large nucleotide-dependent conformational change in Rab28.,Lee SH, Baek K, Dominguez R FEBS Lett. 2008 Dec 10;582(29):4107-11. Epub 2008 Nov 19. PMID:19026641^[2]

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

References

↑ Roosing S, Rohrschneider K, Beryozkin A, Sharon D, Weisschuh N, Staller J, Kohl S, Zelinger L, Peters TA, Neveling K, Strom TM, van den Born LI, Hoyng CB, Klaver CC, Roepman R, Wissinger B, Banin E, Cremers FP, den Hollander AI. Mutations in RAB28, encoding a farnesylated small GTPase, are associated with autosomal-recessive cone-rod dystrophy. Am J Hum Genet. 2013 Jul 11;93(1):110-7. doi: 10.1016/j.ajhg.2013.05.005. Epub, 2013 Jun 6. PMID:23746546 doi:https://dx.doi.org/10.1016/j.ajhg.2013.05.005
↑ Lee SH, Baek K, Dominguez R. Large nucleotide-dependent conformational change in Rab28. FEBS Lett. 2008 Dec 10;582(29):4107-11. Epub 2008 Nov 19. PMID:19026641 doi:10.1016/j.febslet.2008.11.008

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Roosing S, Rohrschneider K, Beryozkin A, Sharon D, Weisschuh N, Staller J, Kohl S, Zelinger L, Peters TA, Neveling K, Strom TM, van den Born LI, Hoyng CB, Klaver CC, Roepman R, Wissinger B, Banin E, Cremers FP, den Hollander AI. Mutations in RAB28, encoding a farnesylated small GTPase, are associated with autosomal-recessive cone-rod dystrophy. Am J Hum Genet. 2013 Jul 11;93(1):110-7. doi: 10.1016/j.ajhg.2013.05.005. Epub, 2013 Jun 6. PMID:23746546 doi:https://dx.doi.org/10.1016/j.ajhg.2013.05.005

[2] Lee SH, Baek K, Dominguez R. Large nucleotide-dependent conformational change in Rab28. FEBS Lett. 2008 Dec 10;582(29):4107-11. Epub 2008 Nov 19. PMID:19026641 doi:10.1016/j.febslet.2008.11.008

[1]

[2]

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3e5h.jpg|left|200px]]
-<!--
+==Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form==
-The line below this paragraph, containing "STRUCTURE_3e5h", creates the "Structure Box" on the page.
+<StructureSection load='3e5h' size='340' side='right'caption='[[3e5h]], [[Resolution|resolution]] 1.50&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'>[[3e5h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2hy4 2hy4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E5H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E5H 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]] 1.499&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_3e5h|  PDB=3e5h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e5h OCA], [https://pdbe.org/3e5h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e5h RCSB], [https://www.ebi.ac.uk/pdbsum/3e5h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e5h ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/RAB28_HUMAN RAB28_HUMAN] Cone rod dystrophy. The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:23746546</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/RAB28_HUMAN RAB28_HUMAN]
+== 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/e5/3e5h_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=3e5h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rab GTPases are essential regulators of membrane trafficking. We report crystal structures of Rab28 in the active (GppNHp-bound) and inactive (GDP-3'P-bound) forms at 1.5 and 1.1A resolution. Rab28 is a distant member of the Rab family. While the overall fold of Rab28 resembles that of other Rab GTPases, it undergoes a larger nucleotide-dependent conformational change than other members of this family. Added flexibility resulting from a double-glycine motif at the beginning of switch 2 might partially account for this observation. The double-glycine motif, which is conserved in the Arf family, only occurs in Rab28 and Rab7B of the Rab family, and may have a profound effect on their catalytic activities.
-===Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form===
+Large nucleotide-dependent conformational change in Rab28.,Lee SH, Baek K, Dominguez R FEBS Lett. 2008 Dec 10;582(29):4107-11. Epub 2008 Nov 19. PMID:19026641<ref>PMID:19026641</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3e5h" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-E5H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2hy4 2hy4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E5H OCA].
+*[[Ras-related protein Rab 3D structures|Ras-related protein Rab 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Baek, K.]]
+[[Category: Baek K]]
-[[Category: Dominguez, R.]]
+[[Category: Dominguez R]]
-[[Category: Lee, S H.]]
+[[Category: Lee SH]]
-[[Category: Li, Y.]]
+[[Category: Li Y]]
-[[Category: Alternative splicing]]
-[[Category: Cell membrane]]
-[[Category: Gtp-binding]]
-[[Category: Lipoprotein]]
-[[Category: Membrane]]
-[[Category: Nucleotide-binding]]
-[[Category: Prenylation]]
-[[Category: Rab gtpase]]
-[[Category: Signaling protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 27 11:38:51 2008''

3e5h: Difference between revisions

Latest revision as of 12:58, 30 August 2023

Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form

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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