Data DOI: 10.15785/SBGRID/848 | ID: 848
Publication DOI: 10.1038/s41467-021-27287-4
7OTT Coordinates: Viewer, PDB (RCSB) (PDBe), MMDB
Kastritis Laboratory, Martin Luther University Halle-Wittenberg
Release Date: 23 Nov 2021
1. If this dataset is locally available, it should be accessable at /programs/datagrid/848
2. To download this dataset, please run the following command from your Terminal on a Linux or OS X workstation:
'rsync -av rsync://data.sbgrid.org/10.15785/SBGRID/848 .' (Harvard Medical School, USA)
Depending on your location, faster access may be available from a Tier 1 site closer to your location
'rsync -av rsync://sbgrid.icm.uu.se/10.15785/SBGRID/848 .' (Uppsala University, Sweden)
'rsync -av rsync://sbgrid.pasteur.edu.uy/10.15785/SBGRID/848 .' (Institut Pasteur de Montevideo, Uruguay)
'rsync -av rsync://sbgrid.ncpss.org/10.15785/SBGRID/848 .' (Shanghai Institutes for Biological Sciences, China)
3. After the transfer is completed, please issue the following command to verify data integrity:
'cd 848 ; shasum -c files.sha'
Storage requirements: 8.2G
Biological Sample:
PDHc Core Scaffold structure from C. thermophilum
Dataset Type:
Structural Model
Subject Composition:
Protein
Collection Facility:
N/A
Data Creation Date:
1 Jun 2021
Related Datasets:
None
Tueting, C; Kastritis, P. 2021. "PDHc Core Scaffold structure from C. thermophilum. PDB Code 7OTT", SBGrid Data Bank, V1, https://doi.org/10.15785/SBGRID/848.
Structural model of the E3BP core, refined in a C2 symmetrized cryoEM map. E3BP showed a minimal fold, which is conserved, and can be found in various other E2 proteins from diverse acyl-transferases, including the 2-keto acid dehydrogenase family. Additionally, by fitting the structural models into an asymmetrically refined cryoEM map, we supply a structural model for the native core scaffold of the PDHc metabolon from C. thermophilum. Models were built and refined by COOT and PHENIX. To capture the transient interaction of lipoyl domain (LD) and the core structure during the transacetylase reaction, we docked the LDs of C. thermophilum, H. sapiens, and N. crassa to their respective core structure. HADDOCK parameter files are deposited to reproduce docking. The best docking solution of C. thermophilum was used to study the interaction by extensive MD simulations. Parameter files and results are also given, to reproduce these simulations.
| Name | Additional Roles | Affiliation While Working on the Project |
|---|---|---|
| Christian Tueting | Data Collector, Depositor | Martin Luther University Halle-Wittenberg |
| Panagiotis L. Kastritis | PI | Martin Luther University Halle-Wittenberg |
N/A
License: CC0
Terms: Our Community Norms as well as good scientific practices expect that proper credit is given via citation. Please use the data citation, as generated by the SBGrid Data Bank.
