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Ensembles from dynamic refinement of non-phosphorylated and phosphorylated phospholamban-SERCA complexes

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
2021-01-22
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Persistent link to this item

https://doi.org/10.13020/bkja-jq93
 https://hdl.handle.net/11299/218010
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Collection period

2018-08-01
2020-07-01

Date completed

2021-01-20

Date updated

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Source information

Journal Title

Journal ISSN

Volume Title

Title

Ensembles from dynamic refinement of non-phosphorylated and phosphorylated phospholamban-SERCA complexes

Published Date

2021-01-22

Authors

Group

Veglia Lab

Author Contact

Veglia, Gianluigi
vegli001@umn.edu

Type

Dataset
Experimental Data
Simulation Data

Abstract

Analysis, setup and ensembles of the dynamic refinement of phospholamban-SERCA complexes in the calcium-free E2 state. Includes trajectory files, analytic scripts, restraint files, setup files, simulation code, raw data (including OS-ssNMR data) and processed data used for the associated citations as per transparent reporting requirements.

Description

Full GROMACS ensembles of SERCA-PLN and SERCA-pS16PLN complexes (40 ps time-step, 10200 frames, 400 ns) - SERCA_PLN_E2_apo_Ensemble (6.6 GB). Topology file: SERCA_PLN_E2_apo_frame0.gro (7.8 MB) - SERCA_PLN_E2_pS16_Ensemble.xtc (6.6 GB). Topology file: SERCA_PLN_E2_pS16_frame0.gro (7.8 MB) Stripped GROMACS ensembles of SERCA-PLN and SERCA-pS16PLN complexes (40 ps time-step, 10200 frames, 400 ns) - no water or lipids - nonP_PLN_SERCA_E2_8rep_dt40.xtc (633.8 MB). Topology file: nonP_PLN_SERCA_E2.gro (735.9 kB) - pS16_PLN_SERCA_E2_8rep_dt40.xtc (634.1 MB). Topology file: pS16_PLN_SERCA_E2.gro (736.0 kB) Configuration and restraint files use to generate ensembles Analytical scripts and processed data for: - Principal component analysis - Distance measurements - Contact analysis - Helix allostery Raw experimental data: - All SE-SAMPI4 spectra of PLN and pPLN alone and in complex with SERCA - Raw FID files - Processing script (NMRPipe) - Assignments

Referenced by

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

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License

CC0 1.0 Universal
 http://creativecommons.org/publicdomain/zero/1.0/

Publisher

Collections

Data Repository for U of M (DRUM)

Funding information

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

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Previously Published Citation

Other identifiers

Suggested citation

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 complexes. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/bkja-jq93.

View/Download File

File View/Open
Description
Size
SERCA_PLN_E2_apo_frame0.gro
GROMACS topology file for full ensemble of non-phosphorylated SERCA-PLN complex
(7.45 MB)

SERCA_PLN_E2_apo_Ensemble.xtc
Full ensemble of non-phosphorylated SERCA-PLN complex. GROMACS trajectory.
(6.15 GB)

SERCA_PLN_E2_pS16_frame0.gro
GROMACS topology file for full ensemble of phosphorylated SERCA-PLN complex
(7.45 MB)

SERCA_PLN_E2_pS16_Ensemble.xtc
Full ensemble of phosphorylated SERCA-PLN complex. GROMACS trajectory.
(6.15 GB)

nonP_PLN_SERCA_E2.gro
GROMACS topology file for stripped ensemble (no water or lipids) of non-phosphorylated SERCA-PLN complex
(718.66 KB)

nonP_PLN_SERCA_E2_8rep_dt40.xtc
Stripped ensemble (no water or lipids) of non-phosphorylated SERCA-PLN complex. GROMACS trajectory.
(604.47 MB)

pS16_PLN_SERCA_E2.gro
GROMACS topology file for stripped ensemble (no water or lipids) of phosphorylated SERCA-PLN complex
(718.79 KB)

pS16_PLN_SERCA_E2_8rep_dt40.xtc
Stripped ensemble (no water or lipids) of phosphorylated SERCA-PLN complex. GROMACS trajectory.
(604.71 MB)

representativeStructures_serca-afa.zip
Representative structures of non-phosphorylated SERCA-PLN complex by cluster. PDB format.
(27.34 MB)

representativeStructures_serca-ps16.zip
Representative structures of phosphorylated SERCA-PLN complex by cluster. PDB format.
(55.03 MB)

analysis_PCA_and_Clustering.zip
Principal component analysis and clustering.
(277.7 MB)

analysis_HelixAllostery.zip
Helix allostery analysis
(27.39 MB)

analysis_HeadPieceDistances.zip
Headpiece distance measurements
(2.49 MB)

analysis_Contacts.zip
Contact analysis
(6.91 MB)

analysis_CheckRestraints.zip
Distance measurements and comparison to experimental OS-ssNMR restraints
(92.48 MB)

restraints_RAOR-MD.zip
GROMACS restraint and configuration files for RAOR-MD.
(5.76 KB)

data_OS-ssNMR.zip
OS-ssNMR data - All SE-SAMPI4 spectra. Raw and processed (NMRPipe) data. Assigned spectra (SPARKY).
(22.76 MB)

FileDirectory.txt
File directory
(48.74 KB)

Readme.txt
Readme
(10.69 KB)

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