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Sandbox 154

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Revision as of 08:51, 26 March 2010

2zwh, resolution 3.30Å ()

Ligands:

Non-Standard Residues:

Structural annotation:
Resources:	InterPro : Ipr004000, Ipr020902, Ipr004001 Pfam : PF00022 UniProt : P68135

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

1 F-Actin

F-Actin

Filamentous actin (F-actin) is also referred to as microfilament ^[1] and is a highly conserved proteinous component found near ubiquitously in eukaryotic cytoskeletons. F-actin and other actin proteins generally provide a structural role to the cell.

Introduction

Actin is found in nearly all eukaryotic cells and is known primarily for its function as a structural and translocation protein. It also has an ATPase function, as it hydrolyzes ATP --> ADP + Pi and undergoes conformational changes with each hydrolysis. Actin belongs to the actin superfamily, which includes other proteins such as Hsp70 and hexokinase, because of its nucelotide-dependent conformational change reference Graceffa. Prokaryotes are not known to have actin, but do however have an actin homologue, MreB reference

Actin occurs in two forms: globular actin (G-actin), the free monomeric units of actin, and filamentous actin (F-actin) which is the polymer form. These two forms exist in a dynamic equilibrium with one another as ATP-associated polymerization and depolymerization occur continuously within the cell.

Assembly

Monomeric Unit - G-actin

G-actin is the free monomeric form of actin which transitions to F-actin. The structures of globular and filamentous actin are distinct from one another in numerous ways, despite the fact that G-actin comprises F-actin. When the monomeric actin becomes polymerized into F-actin, the unit becomes flattened. G-actin appears to have more ion ligands in its structure, and also has the ligand RHO as opposed to 4-methyl histidine as found in the F-actin structure.

Structure

History of the structure

The F-actin protein was discovered by Straub in 1942. The structure was speculated based on a low-resolution x-ray crystallograph found in 1990 by Holmes et al. and over this time, despite the importance of F-actin in eukaryotic cells, this speculated structure was accepted. A higher resolution structure was only recently deposited in the PDB databank in Decemeber 2008 by Oda et al. ^[2].

Polymer F-actin

F-actin has the appearance of two right-handed helices. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å. ^[3]. Including the ADP and Ca²⁺, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft^[4]. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft^[5]. Domain movement is made possible by the rotation about the shown in purple.

Domains

Function

Enzymatic Role

Active Site

Ligand

Structural Role

References

↑ Microfilament - Wikipedia, the free encyclopedia. http://en.wikipedia.org/wiki/Microfilaments. Date accessed: March 16th, 2010.
↑ Oda T, Iwasa M, Aihara T, Maéda Y, and Narita A. 2009. The nature of the globular-to fibrous actin transition. Nature,457(7228):441-445. PMID: 19158791
↑ Holmes, K.C., Popp, D., Gebhard, W. and Kabsch, W. 1990. Atomic model of the actin filament. Nature,347(6288):44-49. PMID: 2395461
↑ oda
↑ pfaendtner

Please do NOT make changes to this Sandbox until after April 23, 2010. Sandboxes 151-200 are reserved until then for use by the Chemistry 307 class at UNBC taught by Prof. Andrea Gorrell.

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_154"

@@ Line 9: / Line 9: @@
 == Assembly ==
-<applet load='1j6z' size='175' color='black' frame='true' align='right' caption='Globular Actin (G-actin): PDB identifier [http://www.rcsb.org/pdb/explore/explore.do?structureId=1J6Z/ 1J6Z].'scene='Sandbox_154/1j6z_black/1'/>
+<applet load='1j6z' size='175' color='black' frame='true' align='right' caption='Globular Actin (G-actin): PDB identifier [http://www.rcsb.org/pdb/explore/explore.do?structureId=1J6Z/ 1J6Z].' scene='Sandbox_154/1j6z_black/1'/>
 === Monomeric Unit - G-actin  ===
 G-actin is the free monomeric form of actin which transitions to F-actin. The structures of globular and filamentous actin are distinct from one another in numerous ways, despite the fact that G-actin comprises F-actin. When the monomeric actin becomes polymerized into F-actin, the unit becomes flattened. G-actin appears to have more <scene name='Sandbox_154/1j6z_calcium/1'>Ca2+</scene> ion ligands in its structure, and also has the ligand RHO as opposed to 4-methyl histidine as found in the F-actin structure.
@@ Line 18: / Line 18: @@
 === History of the structure ===
 The F-actin protein was discovered by Straub in 1942. The structure was speculated based on a low-resolution x-ray crystallograph found in 1990 by Holmes et al. and over this time, despite the importance of F-actin in eukaryotic cells, this speculated structure was accepted. A higher resolution structure was only recently deposited in the PDB databank in Decemeber 2008 by Oda et al. <ref> Oda T, Iwasa M, Aihara T, Maéda Y, and Narita A. 2009. The nature of the globular-to fibrous actin transition. Nature,457(7228):441-445. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19158791/ 19158791]</ref>.
 === Polymer F-actin ===
 <applet load='2zwh' size='200' color='black' frame='true' align='left' caption='Filamentous Actin (F-actin)' scene='Sandbox_154/2zwh_black_domains/1'/>
-<scene name='Sandbox_154/Thing_in_the_middle/1'>This thing in the middle</scene>
+F-actin has the appearance of two right-handed helices. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å. <ref> Holmes, K.C., Popp, D., Gebhard, W. and Kabsch, W. 1990. Atomic model of the actin filament. Nature,347(6288):44-49. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2395461/ 2395461]</ref>. Including the ADP and Ca<sup>2+</sup>, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft<ref>oda</ref>. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft<ref>pfaendtner</ref>. Domain movement is made possible by the rotation about the <scene name='Sandbox_154/2zwh_helix_domains_2/1'> 141-142 and 335-336 residue bonds</scene> shown in purple.
-F-actin has the appearance of two right-handed helices. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å. <ref> Holmes, K.C., Popp, D., Gebhard, W. and Kabsch, W. 1990. Atomic model of the actin filament. Nature,347(6288):44-49. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2395461/ 2395461]</ref>. Including the ADP and Ca<sup>2+</sup>, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft<ref>oda</ref>. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft<ref>pfaendtner</ref>. Domain movement is made possible by the rotation about the <scene name='Sandbox_154/2zwh_helix_domains/1'> 141-142 and 335-336 residue bonds</scene> shown in purple.