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.


2or1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:05, 21 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2or1.jpg|left|200px]]
 
-
{{Structure
+
==RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION==
-
|PDB= 2or1 |SIZE=350|CAPTION= <scene name='initialview01'>2or1</scene>, resolution 2.500&Aring;
+
<StructureSection load='2or1' size='340' side='right'caption='[[2or1]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
+
<table><tr><td colspan='2'>[[2or1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OR1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OR1 FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-
|GENE=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2or1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2or1 OCA], [https://pdbe.org/2or1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2or1 RCSB], [https://www.ebi.ac.uk/pdbsum/2or1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2or1 ProSAT]</span></td></tr>
-
|DOMAIN=
+
</table>
-
|RELATEDENTRY=
+
== Function ==
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2or1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2or1 OCA], [http://www.ebi.ac.uk/pdbsum/2or1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2or1 RCSB]</span>
+
[https://www.uniprot.org/uniprot/RPC1_BP434 RPC1_BP434] Binds to two sets of three contiguous operator sites in the phage genome.
-
}}
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
'''RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION'''
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
 
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/or/2or1_consurf.spt"</scriptWhenChecked>
-
==Overview==
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
The repressors of temperate bacteriophages such as 434 and lambda control transcription by binding to a set of DNA operator sites. The different affinity of repressor for each of these sites ensures efficient regulation. High-resolution x-ray crystallography was used to study the DNA-binding domain of phage 434 repressor in complex with a synthetic DNA operator. The structure shows recognition of the operator by direct interactions with base pairs in the major groove, combined with the sequence-dependent ability of DNA to adopt the required conformation on binding repressor. In particular, a network of three-centered bifurcated hydrogen bonds among base pairs in the operator helps explain why 434 repressor prefers certain sites over others. These bonds, which stabilize the conformation of the bound DNA, can form only with certain sequences.
+
<text>to colour the structure by Evolutionary Conservation</text>
-
 
+
</jmolCheckbox>
-
==About this Structure==
+
</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=2or1 ConSurf].
-
2OR1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Phage_434 Phage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OR1 OCA].
+
<div style="clear:both"></div>
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Recognition of a DNA operator by the repressor of phage 434: a view at high resolution., Aggarwal AK, Rodgers DW, Drottar M, Ptashne M, Harrison SC, Science. 1988 Nov 11;242(4880):899-907. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3187531 3187531]
+
[[Category: Large Structures]]
[[Category: Phage 434]]
[[Category: Phage 434]]
-
[[Category: Single protein]]
+
[[Category: Aggarwal AK]]
-
[[Category: Aggarwal, A K.]]
+
[[Category: Drottar M]]
-
[[Category: Drottar, M.]]
+
[[Category: Harrison SC]]
-
[[Category: Harrison, S C.]]
+
[[Category: Ptashne M]]
-
[[Category: Ptashne, M.]]
+
[[Category: Rodgers DW]]
-
[[Category: Rodgers, D W.]]
+
-
[[Category: double helix]]
+
-
[[Category: protein-dna complex]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:21:55 2008''
+

Current revision

RECOGNITION OF A DNA OPERATOR BY THE REPRESSOR OF PHAGE 434. A VIEW AT HIGH RESOLUTION

PDB ID 2or1

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/2or1"
Personal tools