This codebook.txt file was generated on 2021-01-22 by Katie Barrick ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Ensembles from dynamic refinement of non-phosphorylated and phosphorylated phospholamban-SERCA complex 2. Author Information Principal Investigator Contact Information Name: Gianluigi Veglia Institution: University of Minnesota Email: vegli001@umn.edu Associate or Co-investigator Contact Information Name: Máximo Sanz-Hernández Institution: Imperial College London Associate or Co-investigator Contact Information Name: Venkateswara Reddy Uddigiri Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Songlin Wang Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Erik K. Larsen Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Tata Gopinath Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Martin Gustavsson Institution: University of Copenhagen Associate or Co-investigator Contact Information Name: Razvan L. Cornea Institution: University of Minnesota Associate or Co-investigator Contact Information Name: David D. Thomas Institution: University of Minnesota Associate or Co-investigator Contact Information Name: Alfonso De Simone Institution: Imperial College London, University of Naples “Federico II” Associate or Co-investigator Contact Information Name: Daniel K. Weber Institution: University of Minnesota 3. Date of data collection: 2018-08-01 to 2020-07-01 4. Geographic location of data collection (where was data collected?): NMR data: Minnesota NMR Center, University of Minnesota RAOR-MD data: Imperial College London 5. Information about funding sources that supported the collection of the data: Sponsorship: National Institutes of Health R01GM064742; National Institutes of Health R01HL144100; National Institutes of Health R01HL139065; National Institutes of Health R37AG026160; American Heart Association Postdoctoral Fellowship 19POST34420009; European Research Council CoG - BioDisOrder 819644 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal 2. Links to publications that cite or use the data: Weber, D. K., Sanz-Hernández, M., Reddy, U. V., Wang, S., Larsen, E. K., Gopinath, T., ... & Veglia, G. Structural Basis for Allosteric Control of the SERCA-Phospholamban Membrane Complex by Ca2+ and cAMP-dependent Phosphorylation. bioRxiv, 2020-08. https://doi.org/10.1101/2020.08.28.271940 3. Links to other publicly accessible locations of the data: GROMACS patch for applying relpica-averaged orientational restraints: https://github.com/maximosanz/modelSSNMR 4. Links/relationships to ancillary data sets: Biological Magnetic Resonance Data Bank (https://bmrb.io/) - Deposition of data_OS-ssNMR.zip in progress. 5. Was data derived from another source? If yes, list source(s): No 6. Recommended citation for the data: Weber, Daniel K; Sanz-Hernández, Máximo; Uddigiri, Venkateswara Reddy; Wang, Songlin; Larsen, Erik K; Gopinath, Tata; Gustavsson, Martin; Cornea, Razvan L; Thomas, David D; De Simone, Alfonso; Veglia, Gianluigi. (2021). Ensembles from dynamic refinement of non-phosphorylated and phosphorylated phospholamban-SERCA complex. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/218010. https://doi.org/10.13020/bkja-jq93 --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: nonP_PLN_SERCA_E2_8rep_dt40.xtc Short description: Stripped ensemble (no water or lipids) of non-phosphorylated SERCA-PLN complex. GROMACS trajectory. B. Filename: pS16_PLN_SERCA_E2_8rep_dt40.xtc Short description: Stripped ensemble (no water or lipids) of phosphorylated SERCA-PLN complex. GROMACS trajectory. C. Filename: SERCA_PLN_E2_apo_Ensemble.xtc Short description: Full ensemble of non-phosphorylated SERCA-PLN complex. GROMACS trajectory. D. Filename: SERCA_PLN_E2_pS16_Ensemble.xtc Short description: Full ensemble of phosphorylated SERCA-PLN complex. GROMACS trajectory. E. Filename: nonP_PLN_SERCA_E2.gro Short description: GROMACS topology file for stripped ensemble (no water or lipids) of non-phosphorylated SERCA-PLN complex. F. Filename: pS16_PLN_SERCA_E2.gro Short description: GROMACS topology file for stripped ensemble (no water or lipids) of phosphorylated SERCA-PLN complex. G. Filename: SERCA_PLN_E2_apo_frame0.gro Short description: GROMACS topology file for full ensemble of non-phosphorylated SERCA-PLN complex. H. Filename: SERCA_PLN_E2_pS16_frame0.gro Short description: GROMACS topology file for full ensemble of phosphorylated SERCA-PLN complex. I. Filename: analysis_CheckRestraints.zip Short description: Distance measurements and comparison to experimental OS-ssNMR restraints. J. Filename: analysis_Contacts.zip Short description: Contact analysis of ensembles. K. Filename: analysis_HeadPieceDistances.zip Short description: SERCA Headpiece distance measurements of ensembles. L. Filename: analysis_HelixAllostery.zip Short description: Helix allostery analysis of ensembles. M. Filename: analysis_PCA_and_Clustering.zip Short description: Principal component analysis and clustering of ensembles. N. Filename: data_OS-ssNMR.zip Short description: OS-ssNMR data. All SE-SAMPI4 spectra. Raw and processed (NMRPipe) data. Assigned spectra (SPARKY). O. Filename: representativeStructures_serca-afa.zip Short description: Representative structures of non-phosphorylated SERCA-PLN complex by PCA cluster. PDB format. P. Filename: representativeStructures_serca-ps16.zip Short description: Representative structures of phosphorylated SERCA-PLN complex by PCA cluster. PDB format. Q. Filename: restraints_RAOR-MD.zip Short description: GROMACS restraint and configuration files for RAOR-MD. 2. Relationship between files: data_OS-ssNMR.zip: Raw experimental results used to derive restraints for restraints_RAOR-MD.zip restraints_RAOR-MD.zip: Used to generate ensembles SERCA_PLN_E2_apo_Ensemble.xtc and SERCA_PLN_E2_pS16_Ensemble.xtc. Uses experimental data data_OS-ssNMR.zip SERCA_PLN_E2_apo_frame0.gro, SERCA_PLN_E2_pS16_frame0.gro: Topology files for SERCA_PLN_E2_apo_Ensemble.xtc and SERCA_PLN_E2_pS16_Ensemble.xtc nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc: SERCA_PLN_E2_apo_Ensemble.xtc and SERCA_PLN_E2_pS16_Ensemble.xtc stipped of water and lipids nonP_PLN_SERCA_E2.gro, pS16_PLN_SERCA_E2.gro: Topology files for nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc analysis_CheckRestraints.zip: Analysis of nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc analysis_Contacts.zip: Analysis of nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc analysis_HeadPieceDistances.zip: Analysis of nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc analysis_HelixAllostery.zip: Analysis of nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc analysis_PCA_and_Clustering.zip: Analysis of nonP_PLN_SERCA_E2_8rep_dt40.xtc, pS16_PLN_SERCA_E2_8rep_dt40.xtc representativeStructures_serca-afa.zip: Summarized from non-phosphorylated ensembles in analysis_PCA_and_Clustering.zip representativeStructures_serca-ps16.zip: Summarized from phosphorylated ensembles in analysis_PCA_and_Clustering.zip 3. Additional related data collected that was not included in the current data package: None 4. Are there multiple versions of the dataset? No If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Fully detailed in associated citation. 2. Methods for processing the data: Fully detailed in associated citation. All processing files are included. 3. Instrument- or software-specific information needed to interpret the data: Varian VNMRS spectrometer: Acquisition of NMR data. GROMACS: Computation of ensembles using experimental restraints. NMRPipe: Processing and visualization of experimental NMR data. NMRFAM-SPARKY: Visualization and analysis of experimental NMR data. Visual Molecular Dynamics (VMD): Analysis of structural ensembles. PyMol: Generation of publication-quality images from structural ensembles. Python: Plotting and post-processing (requires packages: Matplotlib, Nmrglue, Numpy). 4. Standards and calibration information, if appropriate: Fully detailed in associated citation. 5. Environmental/experimental conditions: Fully detailed in associated citation. 6. Describe any quality-assurance procedures performed on the data: Fully detailed in associated citation. 7. People involved with sample collection, processing, analysis and/or submission: Daniel K. Weber: Collection and processing of experimental NMR data. Analysis of ensembles. Submission of data. Gianluigi Veglia: Submission of data. Tata Gopinath, Songlin Wang, Venkateswara Reddy Uddigiri, Erik K. Larsen: Collection and processing of experimental NMR data. Máximo Sanz-Hernández: RAOR-MD calculation of ensembles. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [FILENAME] IRRELEVANT SECTION ----------------------------------------- 1. Number of variables: 2. Number of cases/rows: 3. Missing data codes: Code/symbol Definition Code/symbol Definition 4. Variable List Example. Name: Gender Description: Gender of respondent 1 = Male 2 = Female 3 = Other A. Name: Description: Value labels if appropriate B. Name: Description: Value labels if appropriate