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3uf1

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3uf1, resolution 2.81Å ()
Non-Standard Residues:
Gene: VIM (Homo sapiens)
Related: 3ol1


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Crystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural Genomics Consortium Target HR4796B

Publication Abstract from PubMed

Despite the passage of approximately 30 years since the complete primary sequence of the intermediate filament (IF) protein vimentin was reported, the structure remains unknown for both an individual protomer and the assembled filament. In this report, we present data describing the structure of vimentin linker 1 (L1) and rod 1B. Electron paramagnetic resonance spectra collected from samples bearing site-directed spin labels demonstrate that L1 is not a flexible segment between coiled-coils (CCs) but instead forms a rigid, tightly packed structure. An x-ray crystal structure of a construct containing L1 and rod 1B shows that it forms a tetramer comprising two equivalent parallel CC dimers that interact with one another in the form of a symmetrical anti-parallel dimer. Remarkably, the parallel CC dimers are themselves asymmetrical, which enables them to tetramerize rather than undergoing higher order oligomerization. This functionally vital asymmetry in the CC structure, encoded in the primary sequence of rod 1B, provides a striking example of evolutionary exploitation of the structural plasticity of proteins. EPR and crystallographic data consistently suggest that a very short region within L1 represents a minor local distortion in what is likely to be a continuous CC from the end of rod 1A through the entirety of rod 1B. The concordance of this structural model with previously published cross-linking and spectral data supports the conclusion that the crystallographic oligomer represents a native biological structure.

The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and X-ray crystallography., Aziz A, Hess JF, Budamagunta MS, Voss JC, Kuzin AP, Huang YJ, Xiao R, Montelione GT, FitzGerald PG, Hunt JF, J Biol Chem. 2012 Aug 17;287(34):28349-61. doi: 10.1074/jbc.M111.334011. Epub, 2012 Jun 26. PMID:22740688

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

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]

About this Structure

3uf1 is a 4 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 3ol1. Full crystallographic information is available from OCA.

Reference

  1. 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
  2. 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

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