1jff: Difference between revisions
New page: left|200px<br /><applet load="1jff" size="450" color="white" frame="true" align="right" spinBox="true" caption="1jff, resolution 3.5Å" /> '''Refined structure of ... |
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[[Image:1jff.gif|left|200px]]<br /><applet load="1jff" size=" | [[Image:1jff.gif|left|200px]]<br /><applet load="1jff" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1jff, resolution 3.5Å" /> | caption="1jff, resolution 3.5Å" /> | ||
'''Refined structure of alpha-beta tubulin from zinc-induced sheets stabilized with taxol'''<br /> | '''Refined structure of alpha-beta tubulin from zinc-induced sheets stabilized with taxol'''<br /> | ||
==Overview== | ==Overview== | ||
We present a refined model of the alpha beta-tubulin dimer to 3.5 A | We present a refined model of the alpha beta-tubulin dimer to 3.5 A resolution. An improved experimental density for the zinc-induced tubulin sheets was obtained by adding 114 electron diffraction patterns at 40-60 degrees tilt and increasing the completeness of structure factor amplitudes to 84.7 %. The refined structure was obtained using maximum-likelihood including phase information from experimental images, and simulated annealing Cartesian refinement to an R-factor of 23.2 and free R-factor of 29.7. The current model includes residues alpha:2-34, alpha:61-439, beta:2-437, one molecule of GTP, one of GDP, and one of taxol, as well as one magnesium ion at the non-exchangeable nucleotide site, and one putative zinc ion near the M-loop in the alpha-tubulin subunit. The acidic C-terminal tails could not be traced accurately, neither could the N-terminal loop including residues 35-60 in the alpha-subunit. There are no major changes in the overall fold of tubulin with respect to the previous structure, testifying to the quality of the initial experimental phases. The overall geometry of the model is, however, greatly improved, and the position of side-chains, especially those of exposed polar/charged groups, is much better defined. Three short protein sequence frame shifts were detected with respect to the non-refined structure. In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues. | ||
==About this Structure== | ==About this Structure== | ||
1JFF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with ZN, MG, GTP, GDP and TA1 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | 1JFF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=GTP:'>GTP</scene>, <scene name='pdbligand=GDP:'>GDP</scene> and <scene name='pdbligand=TA1:'>TA1</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JFF OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Bos taurus]] | [[Category: Bos taurus]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Downing, K | [[Category: Downing, K H.]] | ||
[[Category: Li, H.]] | [[Category: Li, H.]] | ||
[[Category: Lowe, J.]] | [[Category: Lowe, J.]] | ||
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[[Category: gtpase]] | [[Category: gtpase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:22:01 2008'' | ||
Revision as of 14:22, 21 February 2008
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Refined structure of alpha-beta tubulin from zinc-induced sheets stabilized with taxol
OverviewOverview
We present a refined model of the alpha beta-tubulin dimer to 3.5 A resolution. An improved experimental density for the zinc-induced tubulin sheets was obtained by adding 114 electron diffraction patterns at 40-60 degrees tilt and increasing the completeness of structure factor amplitudes to 84.7 %. The refined structure was obtained using maximum-likelihood including phase information from experimental images, and simulated annealing Cartesian refinement to an R-factor of 23.2 and free R-factor of 29.7. The current model includes residues alpha:2-34, alpha:61-439, beta:2-437, one molecule of GTP, one of GDP, and one of taxol, as well as one magnesium ion at the non-exchangeable nucleotide site, and one putative zinc ion near the M-loop in the alpha-tubulin subunit. The acidic C-terminal tails could not be traced accurately, neither could the N-terminal loop including residues 35-60 in the alpha-subunit. There are no major changes in the overall fold of tubulin with respect to the previous structure, testifying to the quality of the initial experimental phases. The overall geometry of the model is, however, greatly improved, and the position of side-chains, especially those of exposed polar/charged groups, is much better defined. Three short protein sequence frame shifts were detected with respect to the non-refined structure. In light of the new model we discuss details of the tubulin structure such as nucleotide and taxol binding sites, lateral contacts in zinc-sheets, and the significance of the location of highly conserved residues.
About this StructureAbout this Structure
1JFF is a Protein complex structure of sequences from Bos taurus with , , , and as ligands. Full crystallographic information is available from OCA.
ReferenceReference
Refined structure of alpha beta-tubulin at 3.5 A resolution., Lowe J, Li H, Downing KH, Nogales E, J Mol Biol. 2001 Nov 9;313(5):1045-57. PMID:11700061
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