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- PDB-6hxb: SERCA2a from pig heart -

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Basic information

Entry
Database: PDB / ID: 6hxb
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 / regulation of the force of heart contraction / transition between fast and slow fiber / 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
P-type ATPase, subfamily IIA, SERCA-type / 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, subfamily IIA, SERCA-type / 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 superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsSitsel, A. / Andersen, J.L. / Nissen, P. / Olesen, C.
Funding support Belgium, Denmark, 4items
OrganizationGrant numberCountry
Other governmentVLAIO Belgium
Other governmentThe Danish National Research Foundation - Center for Membrane Pumps in Cells and Disease (PUMPkin) Denmark
Other governmentEuropean Research Council Advanced Research grant BIOMEMOS Denmark
Other privateKaren Elise Jensens Fond Denmark
CitationJournal: Embo J. / Year: 2019
Title: Structures of the heart specific SERCA2a Ca 2+ -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
DepositionOct 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,5026
Polymers109,8371
Non-polymers6655
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-27 kcal/mol
Surface area45490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.995, 51.776, 125.604
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number3
Space group name H-MP121

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 21% PEG2000 monomethyl ether, 20% glycerol, 100 mM NaCl, 5% tert-BuOH and 2.4% Zwittergent-3-08

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→42.7 Å / Num. obs: 12416 / % possible obs: 98.7 % / Redundancy: 3.7 % / Net I/σ(I): 4.2
Reflection shellResolution: 4→4.5 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 4→41.724 Å / SU ML: 0.84 / Cross valid method: FREE R-VALUE / Phase error: 47.34
RfactorNum. reflection% reflection
Rfree0.3544 618 5 %
Rwork0.3098 --
obs-12370 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4→41.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7465 0 35 1 7501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017654
X-RAY DIFFRACTIONf_angle_d0.53310357
X-RAY DIFFRACTIONf_dihedral_angle_d6.6394620
X-RAY DIFFRACTIONf_chiral_restr0.0441216
X-RAY DIFFRACTIONf_plane_restr0.0051317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.40220.41481600.38082867X-RAY DIFFRACTION98
4.4022-5.03830.43271480.31882928X-RAY DIFFRACTION99
5.0383-6.34410.38051550.36522948X-RAY DIFFRACTION99
6.3441-41.72580.30381550.26743009X-RAY DIFFRACTION97

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