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.

5amh

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form

Structural highlights

5amh is a 1 chain structure with sequence from Magnetospirillum gryphiswaldense MSR-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.2Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A4TVL0_9PROT

Publication Abstract from PubMed

Cereblon, a primary target of thalidomide and its derivatives, has been characterized structurally from both bacteria and animals. Especially well studied is the thalidomide binding domain, CULT, which shows an invariable structure across different organisms and in complex with different ligands. Here, based on a series of crystal structures of a bacterial representative, we reveal the conformational flexibility and structural dynamics of this domain. In particular, we follow the unfolding of large fractions of the domain upon release of thalidomide in the crystalline state. Our results imply that a third of the domain, including the thalidomide binding pocket, only folds upon ligand binding. We further characterize the structural effect of the C-terminal truncation resulting from the mental-retardation linked R419X nonsense mutation in vitro and offer a mechanistic hypothesis for its irresponsiveness to thalidomide. At 1.2A resolution, our data provide a view of thalidomide binding at atomic resolution.

Structural dynamics of the cereblon ligand binding domain.,Hartmann MD, Boichenko I, Coles M, Lupas AN, Hernandez Alvarez B PLoS One. 2015 May 29;10(5):e0128342. doi: 10.1371/journal.pone.0128342., eCollection 2015. PMID:26024445^[1]

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

References

↑ Hartmann MD, Boichenko I, Coles M, Lupas AN, Hernandez Alvarez B. Structural dynamics of the cereblon ligand binding domain. PLoS One. 2015 May 29;10(5):e0128342. doi: 10.1371/journal.pone.0128342., eCollection 2015. PMID:26024445 doi:http://dx.doi.org/10.1371/journal.pone.0128342

1 Structural highlights
2 Function
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/5amh"

Categories: Large Structures | Magnetospirillum gryphiswaldense MSR-1 | Hartmann MD | Hernandez Alvarez B | Lupas AN

@@ Line 3: / Line 3: @@
 <StructureSection load='5amh' size='340' side='right'caption='[[5amh]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5amh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Maggm Maggm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5amh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Magnetospirillum_gryphiswaldense_MSR-1 Magnetospirillum gryphiswaldense MSR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ami|5ami]], [[5amj|5amj]], [[5amk|5amk]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EF2:S-THALIDOMIDE'>EF2</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=5amh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amh OCA], [http://pdbe.org/5amh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5amh RCSB], [http://www.ebi.ac.uk/pdbsum/5amh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5amh 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=5amh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amh OCA], [https://pdbe.org/5amh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amh RCSB], [https://www.ebi.ac.uk/pdbsum/5amh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amh ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A4TVL0_9PROT A4TVL0_9PROT]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 21: @@
 ==See Also==
-*[[Ubiquitin protein ligase|Ubiquitin protein ligase]]
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
 == References ==
 <references/>
@@ Line 25: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Maggm]]
+[[Category: Magnetospirillum gryphiswaldense MSR-1]]
-[[Category: Alvarez, B Hernandez]]
+[[Category: Hartmann MD]]
-[[Category: Hartmann, M D]]
+[[Category: Hernandez Alvarez B]]
-[[Category: Lupas, A N]]
+[[Category: Lupas AN]]
-[[Category: Aromatic cage]]
-[[Category: Signaling protein]]
-[[Category: Teratogenicity]]

5amh

From Proteopedia

Current revision

Cereblon isoform 4 from Magnetospirillum gryphiswaldense in complex with Thalidomide, trigonal crystal form

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox