Electron paramagnetic resonance (EPR) spectroscopy of full-length vimentin and X-ray crystallography of vimentin peptides has provided concordant structural data for nearly the entire central rod domain of the protein. In this report, we use a combination of EPR spectroscopy and molecular modeling to determine the structure and dynamics of the missing region and unite the separate elements into a single structure. Validation of the linker 1-2 (L1-2) modeling approach is demonstrated by the close correlation between EPR and X-ray data in the previously solved regions. Importantly, molecular dynamic (MD) simulation of the constructed model agrees with spin label motion as determined by EPR. Furthermore, MD simulation shows L1-2 heterogeneity, with a concerted switching of states among the dimer chains. These data provide the first ever experimentally driven model of a complete intermediate filament rod domain, providing research tools for further modeling and assembly studies.
ID: Jd8BmmXZ
Submitter: David Gae
Submission Date: June 12, 2020, 11:14 a.m.
Version: 1
Sequence of the structural domain covered in this paper. (Rod1B-L12-Rod2) GQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAENTLQSFRQDVDNASLARLDLERKVESLQEEIAFLKKLHEEEIQELQAQIQEQHVQIDVDVSKPDLTAALRDVRQQYESVAAKNLQEAEEWYKSKFADLSEAANRNNDALRQAKQESTEYRRQVQSLTCEVDALK
Number of data points | 3 |
Proteins | Human Vimentin |
Unique complexes | 3 |
Assays/Quantities/Protocols | Experimental Assay: Electron Microscope |
Libraries | Electron microscope of vimentin protofilament data |
Supplemental data | Final restrained structure ; Vimentin complete EPR xray data |
Colors: | D | E | R | H | K | S | T | N | Q | A | V | I | L | M | F | Y | W | C | G | P |
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Structure ID | Release Date | Resolution | Structure Title |
---|---|---|---|
1GK4 | 2001-08-08T00:00:00+0000 | 2.3 | HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2) |
1GK6 | 2001-08-08T00:00:00+0000 | 1.9 | Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B) |
1GK7 | 2001-08-08T00:00:00+0000 | 1.4 | HUMAN VIMENTIN COIL 1A FRAGMENT (1A) |
3G1E | 2009-01-29T00:00:00+0000 | 1.83 | X-ray crystal structure of coil 1A of human vimentin |
3KLT | 2009-11-09T00:00:00+0000 | 2.7 | Crystal structure of a vimentin fragment |
3S4R | 2011-05-20T00:00:00+0000 | 2.45 | Crystal structure of vimentin coil1A/1B fragment with a stabilizing mutation |
3SSU | 2011-07-08T00:00:00+0000 | 2.6 | Crystal structure of vimentin coil1A/1B fragment |
3SWK | 2011-07-14T00:00:00+0000 | 1.7 | Crystal structure of vimentin coil1B fragment |
3TRT | 2011-09-10T00:00:00+0000 | 2.3 | Crystal structure of stabilised vimentin coil2 fragment |
3UF1 | 2011-10-31T00:00:00+0000 | 2.81 | Crystal Structure of Vimentin (fragment 144-251) from Homo sapiens, Northeast Structural Genomics Consortium Target HR4796B |
Percent Identity | Matching Chains | Protein | Accession | Entry Name |
---|---|---|---|---|
100.0 | Human Vimentin | P08670 | VIME_HUMAN | |
93.8 | Human Vimentin | P48616 | VIME_BOVIN | |
98.7 | Human Vimentin | P84198 | VIME_CHLAE | |
98.7 | Human Vimentin | Q4R4X4 | VIME_MACFA | |
98.7 | Human Vimentin | Q5R1W8 | VIME_PANTR | |
97.2 | Human Vimentin | P02543 | VIME_PIG | |
93.6 | Human Vimentin | P31000 | VIME_RAT | |
93.6 | Human Vimentin | P20152 | VIME_MOUSE | |
93.3 | Human Vimentin | P02544 | VIME_MESAU | |
93.2 | Human Vimentin | P48670 | VIME_CRIGR |