5MPM | pdb_00005mpm

SERCA2a from pig heart


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.258 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structures of the heart specific SERCA2a Ca2+-ATPase.

Sitsel, A.De Raeymaecker, J.Drachmann, N.D.Derua, R.Smaardijk, S.Andersen, J.L.Vandecaetsbeek, I.Chen, J.De Maeyer, M.Waelkens, E.Olesen, C.Vangheluwe, P.Nissen, P.

(2019) EMBO J 38

  • DOI: https://doi.org/10.15252/embj.2018100020
  • Primary Citation Related Structures: 
    5MPM, 6HXB

  • PubMed Abstract: 

    The sarcoplasmic/endoplasmic reticulum Ca 2+ -ATPase 2a (SERCA2a) performs active reuptake of cytoplasmic Ca 2+ and is a major regulator of cardiac muscle contractility. Dysfunction or dysregulation of SERCA2a is associated with heart failure, while restoring its function is considered as a therapeutic strategy to restore cardiac performance. However, its structure has not yet been determined. Based on native, active protein purified from pig ventricular muscle, we present the first crystal structures of SERCA2a, determined in the CPA-stabilized E2-AlF4- form (3.3 Å) and the Ca 2+ -occluded [Ca 2 ]E1-AMPPCP form (4.0 Å). The structures are similar to the skeletal muscle isoform SERCA1a pointing to a conserved mechanism. We seek to explain the kinetic differences between SERCA1a and SERCA2a. We find that several isoform-specific residues are acceptor sites for post-translational modifications. In addition, molecular dynamics simulations predict that isoform-specific residues support distinct intramolecular interactions in SERCA2a and SERCA1a. Our experimental observations further indicate that isoform-specific intramolecular interactions are functionally relevant, and may explain the kinetic differences between SERCA2a and SERCA1a.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

Macromolecule Content 

  • Total Structure Weight: 110.34 kDa 
  • Atom Count: 7,686 
  • Modeled Residue Count: 992 
  • Deposited Residue Count: 997 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sarcoplasmic/endoplasmic reticulum calcium ATPase 2997Sus scrofaMutation(s): 0 
EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P11607 (Sus scrofa)
Explore P11607 
Go to UniProtKB:  P11607
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11607
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CZA

Query on CZA



Download:Ideal Coordinates CCD File
C [auth A](6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE
C20 H20 N2 O3
RLOAZVAJNNPPDI-DQYPLSBCSA-N
MGF

Query on MGF



Download:Ideal Coordinates CCD File
B [auth A]TRIFLUOROMAGNESATE
F3 Mg
GJOMWUHGUQLOAC-UHFFFAOYSA-K
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.258 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.349α = 90
b = 253.287β = 100.86
c = 64.981γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
VLAIOBelgium--
The Danish National Research Foundation - Center for Membrane Pumps in Cells and Disease (PUMPkin)Denmark--
European Research Council Advanced Research grant BIOMEMOS--
Karen Elise Jensens Fond--
IWT doctoral grant--

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Structure summary
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary