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- PDB-5mpm: SERCA2a from pig heart -

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Basic information

Entry
Database: PDB / ID: 5mpm
TitleSERCA2a from pig heart
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 2
KeywordsHYDROLASE / Ca2+-ATPase / SERCA
Function / homology
Function and homology information


Reduction of cytosolic Ca++ levels / ER-nucleus signaling pathway / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / Ion homeostasis / T-tubule organization / Ion transport by P-type ATPases / ribbon synapse ...Reduction of cytosolic Ca++ levels / ER-nucleus signaling pathway / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / Ion homeostasis / T-tubule organization / Ion transport by P-type ATPases / ribbon synapse / calcium ion import into sarcoplasmic reticulum / P-type Ca2+ transporter / negative regulation of heart contraction / transition between fast and slow fiber / regulation of the force of heart contraction / cardiac muscle hypertrophy in response to stress / regulation of cardiac muscle contraction by calcium ion signaling / S100 protein binding / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of cardiac muscle cell apoptotic process / autophagosome assembly / sarcoplasmic reticulum membrane / negative regulation of receptor binding / calcium ion transmembrane transport / intracellular calcium ion homeostasis / neuron cellular homeostasis / cellular response to oxidative stress / transmembrane transporter binding / calcium ion binding / enzyme binding / ATP hydrolysis activity / ATP binding
Similarity search - Function
Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus ...Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic transduction domain A / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / haloacid dehalogenase-like hydrolase / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CZA / : / TRIFLUOROMAGNESATE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDrachmann, N.D. / Sitsel, A. / Andersen, J.L. / Nissen, P. / Olesen, C.
Funding support Belgium, Denmark, 5items
OrganizationGrant numberCountry
VLAIO Belgium
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
CitationJournal: Embo J. / Year: 2019
Title: Structures of the heart specific SERCA2a Ca2+-ATPase.
Authors: 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.
History
DepositionDec 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,3426
Polymers109,8371
Non-polymers5055
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-13 kcal/mol
Surface area44260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.349, 253.287, 64.981
Angle α, β, γ (deg.)90.00, 100.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 / SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum type / slow twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca(2+) ATPase


Mass: 109836.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P11607, EC: 3.6.3.8

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#3: Chemical ChemComp-CZA / (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


Mass: 336.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 80 mM KCl, 15 mM MgCl2, 2 mM EGTA, 10 mM NaF, 200 uM CPA

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→63.32 Å / Num. obs: 25135 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.082 / Rrim(I) all: 0.155 / Net I/σ(I): 7.1
Reflection shellResolution: 3.3→3.35 Å / Redundancy: 3.6 % / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FGO

3fgo


Resolution: 3.3→63.32 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.25
RfactorNum. reflection% reflection
Rfree0.2579 1937 7.73 %
Rwork0.2041 --
obs0.2083 25045 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→63.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7649 0 32 5 7686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057838
X-RAY DIFFRACTIONf_angle_d0.43110617
X-RAY DIFFRACTIONf_dihedral_angle_d17.2932912
X-RAY DIFFRACTIONf_chiral_restr0.0571242
X-RAY DIFFRACTIONf_plane_restr0.0041355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38250.41991240.3151661X-RAY DIFFRACTION99
3.3825-3.4740.39721480.3261623X-RAY DIFFRACTION98
3.474-3.57620.35811560.30131657X-RAY DIFFRACTION99
3.5762-3.69160.37741570.28311572X-RAY DIFFRACTION98
3.6916-3.82360.33051230.25061711X-RAY DIFFRACTION98
3.8236-3.97660.32121190.28331594X-RAY DIFFRACTION96
3.9766-4.15760.29991330.2251655X-RAY DIFFRACTION99
4.1576-4.37670.25111410.19041644X-RAY DIFFRACTION99
4.3767-4.65090.23841300.17051676X-RAY DIFFRACTION100
4.6509-5.00980.21021340.15541683X-RAY DIFFRACTION100
5.0098-5.51370.23971430.18051646X-RAY DIFFRACTION100
5.5137-6.31090.22941370.20161672X-RAY DIFFRACTION100
6.3109-7.94860.24921370.19651663X-RAY DIFFRACTION99
7.9486-63.33340.18961550.15771651X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.09670.40561.77115.3091-0.36763.49660.0379-0.24290.0956-0.0921-0.0904-0.2536-0.11-0.19740.11430.7634-0.03610.31880.5725-0.04370.6047-0.323365.5322-42.7474
24.143-0.0596-0.16194.3396-0.17594.2019-0.2031-0.0336-0.245-0.39890.00630.28850.2255-0.52730.16430.6172-0.13010.15540.4585-0.04180.6373-22.764952.0827-59.0583
32.4863-0.5248-0.13095.8813-1.09081.9470.04010.07040.104-0.27-0.04790.32940.05130.03240.00341.2579-0.10610.2940.676-0.00970.8885-6.138278.6346-76.3965
40.46181.41070.28244.9327-0.4901-0.65310.0433-0.0153-0.2663-0.1850.08350.51590.26620.0127-0.0521.6739-0.11830.34170.8205-0.0751.746-26.32579.3737-56.1821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:42 or resid 125:243)
2X-RAY DIFFRACTION2chain A and (resid 331:359 or resid 605:745)
3X-RAY DIFFRACTION3chain A and (resid 360:604)
4X-RAY DIFFRACTION4chain A and (resid 43:124 or resid 244:330 or resid 746:992)

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