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.


6cqm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:29, 13 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6cqm' size='340' side='right'caption='[[6cqm]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='6cqm' size='340' side='right'caption='[[6cqm]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6cqm]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CQM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CQM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6cqm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CQM FirstGlance]. <br>
-
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RIM1, YCR028C-A, YCR28C-A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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]] 3&#8491;</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=6cqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqm OCA], [http://pdbe.org/6cqm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cqm RCSB], [http://www.ebi.ac.uk/pdbsum/6cqm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqm 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=6cqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqm OCA], [https://pdbe.org/6cqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cqm RCSB], [https://www.ebi.ac.uk/pdbsum/6cqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/RIM1_YEAST RIM1_YEAST]] This protein binds preferentially and cooperatively to single-stranded DNA (ssDNS). Involved in mitochondrial DNA replication. Stimulates PIF1 helicase activity.<ref>PMID:23175612</ref>
+
[https://www.uniprot.org/uniprot/RIM1_YEAST RIM1_YEAST] This protein binds preferentially and cooperatively to single-stranded DNA (ssDNS). Involved in mitochondrial DNA replication. Stimulates PIF1 helicase activity.<ref>PMID:23175612</ref>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Rim1 is the mitochondrial single-stranded DNA binding protein in Saccharomyces cerevisiae and functions to coordinate replication and maintenance of mtDNA. Rim1 can form homo-tetramers in solution and this species has been assumed to be solely responsible for ssDNA binding. We solved structures of tetrameric Rim1 in two crystals forms which differ in the relative orientation of the dimers within the tetramer. In testing whether the different arrangement of the dimers was due to formation of unstable tetramers, we discovered that while Rim1 forms tetramers at high protein concentration, it dissociates into a smaller oligomeric species at low protein concentrations. A single point mutation at the dimer-dimer interface generates stable dimers and provides support for a dimer-tetramer oligomerization model. The presence of Rim1 dimers in solution becomes evident in DNA binding studies using short ssDNA substrates. However, binding of the first Rim1 dimer is followed by binding of a second dimer, whose affinity depends on the length of the ssDNA. We propose a model where binding of DNA to a dimer of Rim1 induces tetramerization, modulated by the ability of the second dimer to interact with ssDNA.
+
-
 
+
-
The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers.,Singh SP, Kukshal V, De Bona P, Antony E, Galletto R Nucleic Acids Res. 2018 Jun 21. pii: 5042044. doi: 10.1093/nar/gky530. PMID:29931186<ref>PMID:29931186</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6cqm" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Single-stranded DNA-binding protein|Single-stranded DNA-binding protein]]
+
*[[Single-stranded DNA-binding protein 3D structures|Single-stranded DNA-binding protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Baker's yeast]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Bona, P D]]
+
[[Category: Saccharomyces cerevisiae S288C]]
-
[[Category: Edwin, A]]
+
[[Category: Bona PD]]
-
[[Category: Galletto, R]]
+
[[Category: Edwin A]]
-
[[Category: Kukshal, V]]
+
[[Category: Galletto R]]
-
[[Category: Lytle, A K]]
+
[[Category: Kukshal V]]
-
[[Category: Singh, S P]]
+
[[Category: Lytle AK]]
-
[[Category: Dna binding protein]]
+
[[Category: Singh SP]]
-
[[Category: Mitochondrial single-stranded dna binding protein]]
+

Current revision

Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, Rim1 (Form2)

PDB ID 6cqm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6cqm"
Personal tools