PDHc Core Scaffold structure from C. thermophilum

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: Nov. 23, 2021

Data Access Instructions

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)

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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:


Collection Facility:


Data Creation Date:

June 1, 2021

Related Datasets:


Cite this Dataset

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.

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Dataset Description

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.

Project Members

Name Additional Roles Affiliation While Working on the Project
Christian TuetingData Collector, DepositorMartin Luther University Halle-Wittenberg
Panagiotis L. KastritisPIMartin Luther University Halle-Wittenberg

Reprocessing Instructions


License and Terms of use

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.