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.

2jf5

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:09, 19 January 2022

crystal structure of Lys63-linked di-ubiquitin

Structural highlights

2jf5 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1c3t, 1d3z, 1f9j, 1fxt, 1g6j, 1gjz, 1nbf, 1ogw, 1q5w, 1s1q, 1sif, 1tbe, 1ubi, 1ubq, 1xd3, 1xqq, 1yx5, 1yx6, 1zgu, 2ayo, 2bgf, 2fcm, 2fcn, 2fcq, 2fcs, 2fuh, 2g45, 2gbk, 2gbm, 2gbn, 2j7q
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

At least eight types of ubiquitin chain exist, and individual linkages affect distinct cellular processes. The only distinguishing feature of differently linked ubiquitin chains is their structure, as polymers of the same unit are chemically identical. Here, we have crystallized Lys 63-linked and linear ubiquitin dimers, revealing that both adopt equivalent open conformations, forming no contacts between ubiquitin molecules and thereby differing significantly from Lys 48-linked ubiquitin chains. We also examined the specificity of various deubiquitinases (DUBs) and ubiquitin-binding domains (UBDs). All analysed DUBs, except CYLD, cleave linear chains less efficiently compared with other chain types, or not at all. Likewise, UBDs can show chain specificity, and are able to select distinct linkages from a ubiquitin chain mixture. We found that the UBAN (ubiquitin binding in ABIN and NEMO) motif of NEMO (NF-kappaB essential modifier) binds to linear chains exclusively, whereas the NZF (Npl4 zinc finger) domain of TAB2 (TAK1 binding protein 2) is Lys 63 specific. Our results highlight remarkable specificity determinants within the ubiquitin system.

Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains.,Komander D, Reyes-Turcu F, Licchesi JD, Odenwaelder P, Wilkinson KD, Barford D EMBO Rep. 2009 May;10(5):466-73. Epub 2009 Apr 17. PMID:19373254^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Komander D, Reyes-Turcu F, Licchesi JD, Odenwaelder P, Wilkinson KD, Barford D. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep. 2009 May;10(5):466-73. Epub 2009 Apr 17. PMID:19373254 doi:10.1038/embor.2009.55

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2jf5"

@@ Line 3: / Line 3: @@
 <StructureSection load='2jf5' size='340' side='right'caption='[[2jf5]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2jf5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JF5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2JF5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2jf5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JF5 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1c3t|1c3t]], [[1d3z|1d3z]], [[1f9j|1f9j]], [[1fxt|1fxt]], [[1g6j|1g6j]], [[1gjz|1gjz]], [[1nbf|1nbf]], [[1ogw|1ogw]], [[1q5w|1q5w]], [[1s1q|1s1q]], [[1sif|1sif]], [[1tbe|1tbe]], [[1ubi|1ubi]], [[1ubq|1ubq]], [[1xd3|1xd3]], [[1xqq|1xqq]], [[1yx5|1yx5]], [[1yx6|1yx6]], [[1zgu|1zgu]], [[2ayo|2ayo]], [[2bgf|2bgf]], [[2fcm|2fcm]], [[2fcn|2fcn]], [[2fcq|2fcq]], [[2fcs|2fcs]], [[2fuh|2fuh]], [[2g45|2g45]], [[2gbk|2gbk]], [[2gbm|2gbm]], [[2gbn|2gbn]], [[2j7q|2j7q]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c3t|1c3t]], [[1d3z|1d3z]], [[1f9j|1f9j]], [[1fxt|1fxt]], [[1g6j|1g6j]], [[1gjz|1gjz]], [[1nbf|1nbf]], [[1ogw|1ogw]], [[1q5w|1q5w]], [[1s1q|1s1q]], [[1sif|1sif]], [[1tbe|1tbe]], [[1ubi|1ubi]], [[1ubq|1ubq]], [[1xd3|1xd3]], [[1xqq|1xqq]], [[1yx5|1yx5]], [[1yx6|1yx6]], [[1zgu|1zgu]], [[2ayo|2ayo]], [[2bgf|2bgf]], [[2fcm|2fcm]], [[2fcn|2fcn]], [[2fcq|2fcq]], [[2fcs|2fcs]], [[2fuh|2fuh]], [[2g45|2g45]], [[2gbk|2gbk]], [[2gbm|2gbm]], [[2gbn|2gbn]], [[2j7q|2j7q]]</div></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=2jf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jf5 OCA], [http://pdbe.org/2jf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jf5 RCSB], [http://www.ebi.ac.uk/pdbsum/2jf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jf5 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=2jf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jf5 OCA], [https://pdbe.org/2jf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jf5 RCSB], [https://www.ebi.ac.uk/pdbsum/2jf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jf5 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 29: / Line 29: @@
 ==See Also==
-*[[Ubiquitin|Ubiquitin]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
 <references/>

2jf5

From Proteopedia

Revision as of 08:09, 19 January 2022

crystal structure of Lys63-linked di-ubiquitin

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox