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.


3dkt

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:24, 20 March 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3dkt.png|left|200px]]
 
-
<!--
+
==Crystal structure of Thermotoga maritima encapsulin==
-
The line below this paragraph, containing "STRUCTURE_3dkt", creates the "Structure Box" on the page.
+
<StructureSection load='3dkt' size='340' side='right'caption='[[3dkt]], [[Resolution|resolution]] 3.10&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'>[[3dkt]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. The June 2009 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DKT 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]] 3.104&#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=3dkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dkt OCA], [https://pdbe.org/3dkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dkt RCSB], [https://www.ebi.ac.uk/pdbsum/3dkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dkt ProSAT]</span></td></tr>
-
{{STRUCTURE_3dkt| PDB=3dkt | SCENE= }}
+
</table>
-
 
+
== Function ==
-
===Crystal structure of Thermotoga maritima encapsulin===
+
[https://www.uniprot.org/uniprot/ENCAP_THEMA ENCAP_THEMA] Shell component of a type 1 encapsulin nanocompartment. Assembles into proteinaceous shells 23-24 nm in diameter with 2-2.5 nm thick walls. Cargo protein Flp (ferritin-like protein, may store iron) is targeted to the interior via its C-terminal extension; empty intact shells can be isolated in the absence of cargo protein (PubMed:19172747, PubMed:27224728, PubMed:32961724, PubMed:30376298, PubMed:33769792, PubMed:33953921, PubMed:34815415). Fe(2+) may be able to pass though the 5-fold and dimer channels in the protein shell (Probable).<ref>PMID:19172747</ref> <ref>PMID:27224728</ref> <ref>PMID:30376298</ref> <ref>PMID:32961724</ref> <ref>PMID:33769792</ref> <ref>PMID:33953921</ref> <ref>PMID:34815415</ref> <ref>PMID:33953921</ref> Protease that exhibits activity toward chymotrypsin and trypsin substrates (PubMed:9872409, PubMed:11210524). Probably does not have antibacterial activity (Probable).<ref>PMID:11210524</ref> <ref>PMID:9872409</ref> <ref>PMID:19172747</ref>
-
 
+
== Evolutionary Conservation ==
-
 
+
[[Image:Consurf_key_small.gif|200px|right]]
-
<!--
+
Check<jmol>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19172747}}, adds the Publication Abstract to the page
+
<jmolCheckbox>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19172747 is the PubMed ID number.
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dk/3dkt_consurf.spt"</scriptWhenChecked>
-
-->
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
{{ABSTRACT_PUBMED_19172747}}
+
<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=3dkt ConSurf].
-
[[3dkt]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_sp. Thermotoga sp.]. The June 2009 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Vaults'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_6 10.2210/rcsb_pdb/mom_2009_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DKT OCA].
+
<div style="clear:both"></div>
-
 
+
== References ==
-
==See Also==
+
<references/>
-
*[[Teaching Scenes%2C Tutorials%2C and Educators' Pages]]
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
[[Category: Large Structures]]
-
<ref group="xtra">PMID:019172747</ref><references group="xtra"/>
+
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
-
[[Category: Thermotoga sp.]]
+
[[Category: Thermotoga maritima]]
[[Category: Vaults]]
[[Category: Vaults]]
-
[[Category: Ban, N.]]
+
[[Category: Ban N]]
-
[[Category: Boehringer, D.]]
+
[[Category: Boehringer D]]
-
[[Category: Gutmann, S.]]
+
[[Category: Gutmann S]]
-
[[Category: Sutter, M.]]
+
[[Category: Sutter M]]
-
[[Category: Weber-Ban, E.]]
+
[[Category: Weber-Ban E]]
-
[[Category: Antibiotic]]
+
-
[[Category: Antimicrobial]]
+
-
[[Category: Bacteriocin]]
+
-
[[Category: Cobalt]]
+
-
[[Category: Enzyme encapsulation]]
+
-
[[Category: Ferritin-like protein]]
+
-
[[Category: Hk97-fold]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nanocompartment]]
+
-
[[Category: Oxidative stress]]
+
-
[[Category: Protease]]
+
-
[[Category: Secreted]]
+
-
[[Category: Structural protein-virus like particle complex]]
+

Current revision

Crystal structure of Thermotoga maritima encapsulin

PDB ID 3dkt

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/3dkt"
Personal tools