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4xok

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Revision as of 23:29, 5 June 2019

Observing the overall rocking motion of a protein in a crystal.

Structural highlights

4xok is a 3 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	UBC (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[UBC_HUMAN] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.^[1] ^[2]

Publication Abstract from PubMed

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall 'rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and mus-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 mus. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Observing the overall rocking motion of a protein in a crystal.,Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier JP, Skrynnikov NR, Schanda P Nat Commun. 2015 Oct 5;6:8361. doi: 10.1038/ncomms9361. PMID:26436197^[3]

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

References

↑ Huang F, Kirkpatrick D, Jiang X, Gygi S, Sorkin A. Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain. Mol Cell. 2006 Mar 17;21(6):737-48. PMID:16543144 doi:S1097-2765(06)00120-1
↑ Komander D. The emerging complexity of protein ubiquitination. Biochem Soc Trans. 2009 Oct;37(Pt 5):937-53. doi: 10.1042/BST0370937. PMID:19754430 doi:10.1042/BST0370937
↑ Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier JP, Skrynnikov NR, Schanda P. Observing the overall rocking motion of a protein in a crystal. Nat Commun. 2015 Oct 5;6:8361. doi: 10.1038/ncomms9361. PMID:26436197 doi:http://dx.doi.org/10.1038/ncomms9361

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/4xok"

@@ Line 1: / Line 1: @@
 ==Observing the overall rocking motion of a protein in a crystal.==
-<StructureSection load='4xok' size='340' side='right' caption='[[4xok]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='4xok' size='340' side='right'caption='[[4xok]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4xok]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XOK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4xok]] is a 3 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=4XOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XOK FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=4xok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xok OCA], [http://pdbe.org/4xok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xok RCSB], [http://www.ebi.ac.uk/pdbsum/4xok PDBsum]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UBC ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4xok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xok OCA], [http://pdbe.org/4xok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xok RCSB], [http://www.ebi.ac.uk/pdbsum/4xok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xok ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 4xok" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ubiquitin|Ubiquitin]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Colletier, J P]]
 [[Category: Coquelle, N]]

4xok

From Proteopedia

Revision as of 23:29, 5 June 2019

Observing the overall rocking motion of a protein in a crystal.

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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