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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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 |