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.




1ph1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:07, 14 February 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ph1.gif|left|200px]]
 
-
<!--
+
==CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGGGT==
-
The line below this paragraph, containing "STRUCTURE_1ph1", creates the "Structure Box" on the page.
+
<StructureSection load='1ph1' size='340' side='right'caption='[[1ph1]], [[Resolution|resolution]] 2.51&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'>[[1ph1]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PH1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PH1 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]] 2.51&#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=1ph1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ph1 OCA], [https://pdbe.org/1ph1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ph1 RCSB], [https://www.ebi.ac.uk/pdbsum/1ph1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ph1 ProSAT]</span></td></tr>
-
{{STRUCTURE_1ph1| PDB=1ph1 | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/TEBA_STENO TEBA_STENO] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.
 +
== 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/ph/1ph1_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=1ph1 ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGGGT'''
+
==See Also==
-
 
+
*[[End-binding protein|End-binding protein]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1PH1 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PH1 OCA].
+
-
 
+
-
==Reference==
+
-
Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes., Theobald DL, Schultz SC, EMBO J. 2003 Aug 15;22(16):4314-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12912928 12912928]
+
-
[[Category: Protein complex]]
+
[[Category: Sterkiella nova]]
[[Category: Sterkiella nova]]
-
[[Category: Schultz, S C.]]
+
[[Category: Schultz SC]]
-
[[Category: Theobald, D L.]]
+
[[Category: Theobald DL]]
-
[[Category: Noncognate]]
+
-
[[Category: Ob fold]]
+
-
[[Category: Oligonucleotide and oligosaccharide binding fold]]
+
-
[[Category: Protein dna interaction]]
+
-
[[Category: Protein/dna]]
+
-
[[Category: Sequence specificity]]
+
-
[[Category: Single strand dna binding protein]]
+
-
[[Category: Telomere]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 05:04:41 2008''
+

Current revision

CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGGGT

PDB ID 1ph1

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/1ph1"
Personal tools