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.

3ax3

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of rat TOM20-ALDH presequence complex: a complex (form2) between Tom20 and a disulfide-bridged presequence peptide containing D-Cys and L-Cys at the i and i+3 positions.

Structural highlights

3ax3 is a 8 chain structure with sequence from Rattus norvegicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ALDH2_RAT

Publication Abstract from PubMed

Most mitochondrial proteins are synthesized in the cytosol and imported into mitochondria. The Tom20 protein, residing on the mitochondrial surface, recognizes the N-terminal presequences of precursor proteins. We previously determined the crystal structures of the Tom20-presequence complex. The successful crystallization involved tethering the presequence to Tom20 through an intermolecular disulfide bond with an optimized linker. In this work, we assessed the tethering method. The intermolecular disulfide bond was cleaved in crystal with a reducing agent. The pose (i.e., conformation and position) of the presequence was identical to the previously determined pose. In another experiment, a longer linker than the optimized length was used for the tethering. The perturbation of the tether changed the pose slightly, but the interaction mode was preserved. These results argue against the forced interaction of the presequence by its covalent attachment to Tom20. Second, as an alternative method referred to as "molecular stiffening", we introduced a disulfide bond within the presequence peptide to restrict the freedom of the peptide in the unbound states. One presequence analogue exhibited over 100-fold higher affinity than its linear counterpart and generated cocrystals with Tom20. One of the two crystallographic snapshots revealed a known pose previously determined by the tethering method, and the other snapshot depicted a new pose. These results confirmed and extended the dynamic, multiple bound state model of the Tom20-presequence interactions and also demonstrated the validity of the molecular tethering and stiffening techniques in studies of transient protein-peptide interactions.

Crystallographic snapshots of tom20-mitochondrial presequence interactions with disulfide-stabilized peptides.,Saitoh T, Igura M, Miyazaki Y, Ose T, Maita N, Kohda D Biochemistry. 2011 Jun 21;50(24):5487-96. Epub 2011 May 26. PMID:21591667^[1]

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

References

↑ Saitoh T, Igura M, Miyazaki Y, Ose T, Maita N, Kohda D. Crystallographic snapshots of tom20-mitochondrial presequence interactions with disulfide-stabilized peptides. Biochemistry. 2011 Jun 21;50(24):5487-96. Epub 2011 May 26. PMID:21591667 doi:10.1021/bi200470x

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ax3"

Categories: Large Structures | Rattus norvegicus | Kohda D | Maita Y | Saitoh T

@@ Line 1: / Line 1: @@
 ==Crystal structure of rat TOM20-ALDH presequence complex: a complex (form2) between Tom20 and a disulfide-bridged presequence peptide containing D-Cys and L-Cys at the i and i+3 positions.==
-<StructureSection load='3ax3' size='340' side='right' caption='[[3ax3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='3ax3' size='340' side='right'caption='[[3ax3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ax3]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AX3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ax3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AX3 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3awr|3awr]], [[3ax2|3ax2]], [[3ax5|3ax5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCY:D-CYSTEINE'>DCY</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></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=3ax3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ax3 OCA], [http://pdbe.org/3ax3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ax3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ax3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ax3 ProSAT]</span></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=3ax3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ax3 OCA], [https://pdbe.org/3ax3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ax3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ax3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ax3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TOM20_RAT TOM20_RAT]] Central component of the receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore (By similarity).
+[https://www.uniprot.org/uniprot/ALDH2_RAT ALDH2_RAT]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Buffalo rat]]
+[[Category: Large Structures]]
-[[Category: Kohda, D]]
+[[Category: Rattus norvegicus]]
-[[Category: Maita, Y]]
+[[Category: Kohda D]]
-[[Category: Saitoh, T]]
+[[Category: Maita Y]]
-[[Category: Membrane protein-transport protein complex]]
+[[Category: Saitoh T]]
-[[Category: Protein-protein complex]]

3ax3

From Proteopedia

Current revision

Crystal structure of rat TOM20-ALDH presequence complex: a complex (form2) between Tom20 and a disulfide-bridged presequence peptide containing D-Cys and L-Cys at the i and i+3 positions.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox