2f4k: Difference between revisions

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{{Seed}}
[[Image:2f4k.png|left|200px]]


<!--
==Chicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9==
The line below this paragraph, containing "STRUCTURE_2f4k", creates the "Structure Box" on the page.
<StructureSection load='2f4k' size='340' side='right'caption='[[2f4k]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2f4k]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F4K FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.05&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene></td></tr>
{{STRUCTURE_2f4k|  PDB=2f4k  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f4k OCA], [https://pdbe.org/2f4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f4k RCSB], [https://www.ebi.ac.uk/pdbsum/2f4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f4k ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/VILI_CHICK VILI_CHICK] Epithelial cell-specific Ca(2+)-regulated actin-modifying protein that modulates the reorganization of microvillar actin filaments. Plays a role in the actin nucleation, actin filament bundle assembly, actin filament capping and severing. Binds phosphatidylinositol 4,5-bisphosphate (PIP2) and lysophosphatidic acid (LPA); binds LPA with higher affinity than PIP2. Binding to LPA increases its phosphorylation by SRC and inhibits all actin-modifying activities. Binding to PIP2 inhibits actin-capping and -severing activities but enhances actin-bundling activity. Regulates the intestinal epithelial cell morphology, cell invasion, cell migration and apoptosis. Protects against apoptosis induced by dextran sodium sulfate (DSS) in the gastrointestinal epithelium. Appears to regulate cell death by maintaining mitochondrial integrity. Enhances hepatocyte growth factor (HGF)-induced epithelial cell motility, chemotaxis and wound repair (By similarity). Its actin-bundling activity is inhibited by tropomyosin.<ref>PMID:3793760</ref> <ref>PMID:1618806</ref>
== 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/f4/2f4k_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f4k ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have investigated the structure, equilibria, and folding kinetics of an engineered 35-residue subdomain of the chicken villin headpiece, an ultrafast-folding protein. Substitution of two buried lysine residues by norleucine residues stabilizes the protein by 1 kcal/mol and increases the folding rate sixfold, as measured by nanosecond laser T-jump. The folding rate at 300 K is (0.7 micros)(-1) with little or no temperature dependence, making this protein the first sub-microsecond folder, with a rate only twofold slower than the theoretically predicted speed limit. Using the 70 ns process to obtain the effective diffusion coefficient, the free energy barrier height is estimated from Kramers theory to be less than approximately 1 kcal/mol. X-ray crystallographic determination at 1A resolution shows no significant change in structure compared to the single-norleucine-substituted molecule and suggests that the increased stability is electrostatic in origin. The ultrafast folding rate, very accurate X-ray structure, and small size make this engineered villin subdomain an ideal system for simulation by atomistic molecular dynamics with explicit solvent.


===Chicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9===
Sub-microsecond protein folding.,Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J J Mol Biol. 2006 Jun 9;359(3):546-53. Epub 2006 Mar 31. PMID:16643946<ref>PMID:16643946</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2f4k" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_16643946}}, adds the Publication Abstract to the page
*[[Villin|Villin]]
(as it appears on PubMed at http://www.pubmed.gov), where 16643946 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_16643946}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Gallus gallus]]
2F4K is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F4K OCA].
[[Category: Large Structures]]
 
[[Category: Chiu TK]]
==Reference==
[[Category: Davies DR]]
<ref group="xtra">PMID:16643946</ref><references group="xtra"/>
[[Category: Eaton WA]]
[[Category: Chiu, T K.]]
[[Category: Hofrichter J]]
[[Category: Davies, D R.]]
[[Category: Kubelka J]]
[[Category: Eaton, W A.]]
[[Category: Hofrichter, J.]]
[[Category: Kubelka, J.]]
[[Category: Villin head group subdomain]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:07:30 2009''

Latest revision as of 12:06, 6 November 2024

Chicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9Chicken villin subdomain HP-35, K65(NLE), N68H, K70(NLE), PH9

Structural highlights

2f4k is a 1 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.05Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VILI_CHICK Epithelial cell-specific Ca(2+)-regulated actin-modifying protein that modulates the reorganization of microvillar actin filaments. Plays a role in the actin nucleation, actin filament bundle assembly, actin filament capping and severing. Binds phosphatidylinositol 4,5-bisphosphate (PIP2) and lysophosphatidic acid (LPA); binds LPA with higher affinity than PIP2. Binding to LPA increases its phosphorylation by SRC and inhibits all actin-modifying activities. Binding to PIP2 inhibits actin-capping and -severing activities but enhances actin-bundling activity. Regulates the intestinal epithelial cell morphology, cell invasion, cell migration and apoptosis. Protects against apoptosis induced by dextran sodium sulfate (DSS) in the gastrointestinal epithelium. Appears to regulate cell death by maintaining mitochondrial integrity. Enhances hepatocyte growth factor (HGF)-induced epithelial cell motility, chemotaxis and wound repair (By similarity). Its actin-bundling activity is inhibited by tropomyosin.[1] [2]

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

We have investigated the structure, equilibria, and folding kinetics of an engineered 35-residue subdomain of the chicken villin headpiece, an ultrafast-folding protein. Substitution of two buried lysine residues by norleucine residues stabilizes the protein by 1 kcal/mol and increases the folding rate sixfold, as measured by nanosecond laser T-jump. The folding rate at 300 K is (0.7 micros)(-1) with little or no temperature dependence, making this protein the first sub-microsecond folder, with a rate only twofold slower than the theoretically predicted speed limit. Using the 70 ns process to obtain the effective diffusion coefficient, the free energy barrier height is estimated from Kramers theory to be less than approximately 1 kcal/mol. X-ray crystallographic determination at 1A resolution shows no significant change in structure compared to the single-norleucine-substituted molecule and suggests that the increased stability is electrostatic in origin. The ultrafast folding rate, very accurate X-ray structure, and small size make this engineered villin subdomain an ideal system for simulation by atomistic molecular dynamics with explicit solvent.

Sub-microsecond protein folding.,Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J J Mol Biol. 2006 Jun 9;359(3):546-53. Epub 2006 Mar 31. PMID:16643946[3]

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

See Also

References

  1. ↑ Burgess DR, Broschat KO, Hayden JM. Tropomyosin distinguishes between the two actin-binding sites of villin and affects actin-binding properties of other brush border proteins. J Cell Biol. 1987 Jan;104(1):29-40. PMID:3793760
  2. ↑ de Arruda MV, Bazari H, Wallek M, Matsudaira P. An actin footprint on villin. Single site substitutions in a cluster of basic residues inhibit the actin severing but not capping activity of villin. J Biol Chem. 1992 Jun 25;267(18):13079-85. PMID:1618806
  3. ↑ Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J. Sub-microsecond protein folding. J Mol Biol. 2006 Jun 9;359(3):546-53. Epub 2006 Mar 31. PMID:16643946 doi:10.1016/j.jmb.2006.03.034

2f4k, resolution 1.05Å

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