1gk6

From Proteopedia

(Difference between revisions)

Current revision

Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)

Structural highlights

1gk6 is a 2 chain structure with sequence from Homo sapiens and Saccharomyces cerevisiae. This structure supersedes the now removed PDB entry 1e7t. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VIME_HUMAN Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally.^[1] Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.^[2] GCN4_YEAST Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'.

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

Intermediate filaments (IFs) are key components of the cytoskeleton in higher eukaryotic cells. The elementary IF 'building block' is an elongated coiled-coil dimer consisting of four consecutive alpha-helical segments. The segments 1A and 2B include highly conserved sequences and are critically involved in IF assembly. Based on the crystal structures of three human vimentin fragments at 1.4-2.3 A resolution (PDB entries 1gk4, 1gk6 and 1gk7), we have established the molecular organization of these two segments. The fragment corresponding to segment 1A forms a single, amphipatic alpha-helix, which is compatible with a coiled-coil geometry. While this segment might yield a coiled coil within an isolated dimer, monomeric 1A helices are likely to play a role in specific dimer-dimer interactions during IF assembly. The 2B segment reveals a double-stranded coiled coil, which unwinds near residue Phe351 to accommodate a 'stutter'. A fragment containing the last seven heptads of 2B interferes heavily with IF assembly and also transforms mature vimentin filaments into a new kind of structure. These results provide the first insight into the architecture and functioning of IFs at the atomic level.

Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly.,Strelkov SV, Herrmann H, Geisler N, Wedig T, Zimbelmann R, Aebi U, Burkhard P EMBO J. 2002 Mar 15;21(6):1255-66. PMID:11889032^[3]

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

References

↑ Challa AA, Stefanovic B. A novel role of vimentin filaments: binding and stabilization of collagen mRNAs. Mol Cell Biol. 2011 Sep;31(18):3773-89. doi: 10.1128/MCB.05263-11. Epub 2011 Jul , 11. PMID:21746880 doi:10.1128/MCB.05263-11
↑ Challa AA, Stefanovic B. A novel role of vimentin filaments: binding and stabilization of collagen mRNAs. Mol Cell Biol. 2011 Sep;31(18):3773-89. doi: 10.1128/MCB.05263-11. Epub 2011 Jul , 11. PMID:21746880 doi:10.1128/MCB.05263-11
↑ Strelkov SV, Herrmann H, Geisler N, Wedig T, Zimbelmann R, Aebi U, Burkhard P. Conserved segments 1A and 2B of the intermediate filament dimer: their atomic structures and role in filament assembly. EMBO J. 2002 Mar 15;21(6):1255-66. PMID:11889032 doi:http://dx.doi.org/10.1093/emboj/21.6.1255

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1gk6"

@@ Line 3: / Line 3: @@
 <StructureSection load='1gk6' size='340' side='right'caption='[[1gk6]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gk6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1e7t 1e7t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GK6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gk6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1e7t 1e7t]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GK6 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1gk4|1gk4]], [[1gk7|1gk7]], [[2zta|2zta]]</div></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]] 1.9&#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=1gk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gk6 OCA], [https://pdbe.org/1gk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gk6 RCSB], [https://www.ebi.ac.uk/pdbsum/1gk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gk6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GCN4_YEAST GCN4_YEAST]] Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'.
+[https://www.uniprot.org/uniprot/VIME_HUMAN VIME_HUMAN] Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally.<ref>PMID:21746880</ref>   Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.<ref>PMID:21746880</ref> [https://www.uniprot.org/uniprot/GCN4_YEAST GCN4_YEAST] Is a transcription factor that is responsible for the activation of more than 30 genes required for amino acid or for purine biosynthesis in response to amino acid or purine starvation. Binds and recognize the DNA sequence: 5'-TGA[CG]TCA-3'.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 30: @@
 ==See Also==
+*[[Gcn4 3D Structures|Gcn4 3D Structures]]
 *[[Gnc4 3D Structures|Gnc4 3D Structures]]
 == References ==
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Aebi, U]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Burkhard, P]]
+[[Category: Aebi U]]
-[[Category: Geisler, N]]
+[[Category: Burkhard P]]
-[[Category: Herrmann, H]]
+[[Category: Geisler N]]
-[[Category: Strelkov, S V]]
+[[Category: Herrmann H]]
-[[Category: Zimbelmann, R]]
+[[Category: Strelkov SV]]
-[[Category: Dimer]]
+[[Category: Zimbelmann R]]
-[[Category: Fusion protein]]
-[[Category: Heptad repeat]]
-[[Category: Intermediate filament]]
-[[Category: Leucine zipper]]
-[[Category: Parallel coiled coil]]
-[[Category: Structural protein]]

1gk6

From Proteopedia

Current revision

Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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