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.


3n4q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:27, 21 February 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='3n4q' size='340' side='right'caption='[[3n4q]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
<StructureSection load='3n4q' size='340' side='right'caption='[[3n4q]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3n4q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hcmvt Hcmvt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N4Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3N4Q FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3n4q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_herpesvirus_5_strain_Towne Human herpesvirus 5 strain Towne]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N4Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N4Q FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.2&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n4p|3n4p]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3n4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n4q OCA], [http://pdbe.org/3n4q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n4q RCSB], [http://www.ebi.ac.uk/pdbsum/3n4q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n4q 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=3n4q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n4q OCA], [https://pdbe.org/3n4q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n4q RCSB], [https://www.ebi.ac.uk/pdbsum/3n4q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n4q ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/TRM3_HCMVA TRM3_HCMVA]] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
+
[https://www.uniprot.org/uniprot/TRM3_HCMVA TRM3_HCMVA] Component of the molecular motor that translocates genomic DNA in empty capsid during DNA packaging. Heterodimerizes with small terminase protein to be docked on capsid portal protein. The latter forms a ring in which genomic DNA in translocated into the capsid. May have or induce an endonuclease activity to cleave the genome concatemer after encapsidation (By similarity).
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
During viral replication, herpesviruses package their DNA into the procapsid by means of the terminase protein complex. In human cytomegalovirus (herpesvirus 5), the terminase is composed of subunits UL89 and UL56. UL89 cleaves the long DNA concatemers into unit-length genomes of appropriate length for encapsidation. We used ESPRIT, a high-throughput screening method, to identify a soluble purifiable fragment of UL89 from a library of 18,432 randomly truncated ul89 DNA constructs. The purified protein was crystallized and its three-dimensional structure was solved. This protein corresponds to the key nuclease domain of the terminase and shows an RNase H/integrase-like fold. We demonstrate that UL89-C has the capacity to process the DNA and that this function is dependent on Mn(2+) ions, two of which are located at the active site pocket. We also show that the nuclease function can be inactivated by raltegravir, a recently approved anti-AIDS drug that targets the HIV integrase.
+
-
 
+
-
Structure and inhibition of herpesvirus DNA packaging terminase nuclease domain.,Nadal M, Mas PJ, Blanco AG, Arnan C, Sola M, Hart DJ, Coll M Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16078-83. Epub 2010 Aug 30. PMID:20805464<ref>PMID:20805464</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3n4q" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
-
*[[Terminase|Terminase]]
+
*[[Terminase 3D Structures|Terminase 3D Structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Hcmvt]]
+
[[Category: Human herpesvirus 5 strain Towne]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Arnan, C]]
+
[[Category: Arnan C]]
-
[[Category: Blanco, A G]]
+
[[Category: Blanco AG]]
-
[[Category: Coll, M]]
+
[[Category: Coll M]]
-
[[Category: Hart, D J]]
+
[[Category: Hart DJ]]
-
[[Category: Mas, P J]]
+
[[Category: Mas PJ]]
-
[[Category: Nadal, M]]
+
[[Category: Nadal M]]
-
[[Category: Sola, M]]
+
[[Category: Sola M]]
-
[[Category: Dna binding protein]]
+
-
[[Category: Dna packaging]]
+
-
[[Category: Hcmv]]
+
-
[[Category: Herpesvirus]]
+
-
[[Category: Human cytomegalovirus]]
+
-
[[Category: Nuclease]]
+
-
[[Category: Terminase]]
+

Current revision

Human cytomegalovirus terminase nuclease domain, Mn soaked

PDB ID 3n4q

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/3n4q"
Personal tools