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.

3l1x

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal Structure of U-box Domain of Human E4B Ubiquitin Ligase

Structural highlights

3l1x is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBE4B_HUMAN Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity).

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

Human E4B, also called UFD2a, is a U box-containing protein that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor. E4B is thought to participate in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. The U box domain is an anchor site for E2 ubiquitin-conjugating enzymes, but little is known of the binding mechanism. Using X-ray crystallography and NMR spectroscopy, we determined the structures of E4B U box free and bound to UbcH5c and Ubc4 E2s. Whereas previously characterized U box domains are homodimeric, we show that E4B U box is a monomer stabilized by a network of hydrogen bonds identified from scalar coupling measurements. These structural studies, complemented by calorimetry- and NMR-based binding assays, suggest an allosteric regulation of UbcH5c and Ubc4 by E4B U box and provide a molecular basis to understand how the ubiquitylation machinery involving E4B assembles.

Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4.,Benirschke RC, Thompson JR, Nomine Y, Wasielewski E, Juranic N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G Structure. 2010 Aug 11;18(8):955-65. PMID:20696396^[1]

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

References

↑ Benirschke RC, Thompson JR, Nomine Y, Wasielewski E, Juranic N, Macura S, Hatakeyama S, Nakayama KI, Botuyan MV, Mer G. Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4. Structure. 2010 Aug 11;18(8):955-65. PMID:20696396 doi:10.1016/j.str.2010.04.017

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3l1x"

Categories: Homo sapiens | Large Structures | Benirschke R | Mer G | Thompson JR

@@ Line 1: / Line 1: @@
 ==Crystal Structure of U-box Domain of Human E4B Ubiquitin Ligase==
-<StructureSection load='3l1x' size='340' side='right' caption='[[3l1x]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='3l1x' size='340' side='right'caption='[[3l1x]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3l1x]] is a 1 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=3L1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3L1X FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3l1x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L1X FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3l1y|3l1y]], [[3l1z|3l1z]]</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]] 2.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBE4B, HDNB1, KIAA0684, UFD2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3l1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1x OCA], [https://pdbe.org/3l1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l1x RCSB], [https://www.ebi.ac.uk/pdbsum/3l1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1x ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3l1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l1x OCA], [http://pdbe.org/3l1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3l1x RCSB], [http://www.ebi.ac.uk/pdbsum/3l1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3l1x ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UBE4B_HUMAN UBE4B_HUMAN]] Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity).
+[https://www.uniprot.org/uniprot/UBE4B_HUMAN UBE4B_HUMAN] Binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3 (By similarity).
 == 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/l1/3l1x_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/3l1x_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Benirschke, R]]
+[[Category: Large Structures]]
-[[Category: Mer, G]]
+[[Category: Benirschke R]]
-[[Category: Thompson, J R]]
+[[Category: Mer G]]
-[[Category: E3 ubiquitin ligase]]
+[[Category: Thompson JR]]
-[[Category: E4 ubiquitin ligase]]
-[[Category: Ligase]]
-[[Category: U-box domain]]
-[[Category: Ubl conjugation pathway]]

3l1x

From Proteopedia

Current revision

Crystal Structure of U-box Domain of Human E4B Ubiquitin Ligase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox