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- PDB-5ztf: Structure of Ca2+ ATPase -

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Basic information

Entry
Database: PDB / ID: 5ztf
TitleStructure of Ca2+ ATPase
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 2
KeywordsHYDROLASE / p-type atpase / calcium transport / endoplasmic reticulum / redox
Function / homology
Function and homology information


longitudinal sarcoplasmic reticulum / 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 / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential ...longitudinal sarcoplasmic reticulum / 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 / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential / ribbon synapse / platelet dense tubular network membrane / calcium ion import into sarcoplasmic reticulum / Pre-NOTCH Processing in Golgi / P-type Ca2+ transporter / sarcoplasmic reticulum calcium ion transport / negative regulation of heart contraction / P-type calcium transporter activity / regulation of the force of heart contraction / transition between fast and slow fiber / cardiac muscle hypertrophy in response to stress / endoplasmic reticulum calcium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / lncRNA binding / S100 protein binding / Reduction of cytosolic Ca++ levels / relaxation of cardiac muscle / positive regulation of heart rate / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of cardiac muscle cell apoptotic process / Ion transport by P-type ATPases / autophagosome assembly / regulation of cardiac conduction / epidermis development / Ion homeostasis / sarcoplasmic reticulum membrane / response to endoplasmic reticulum stress / monoatomic ion transmembrane transport / sarcoplasmic reticulum / negative regulation of receptor binding / calcium ion transmembrane transport / intracellular calcium ion homeostasis / neuron cellular homeostasis / cellular response to oxidative stress / transmembrane transporter binding / cell adhesion / calcium ion binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
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 / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsInoue, M. / Watanabe, S. / Inaba, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR13M6 Japan
CitationJournal: Cell Rep / Year: 2019
Title: Structural Basis of Sarco/Endoplasmic Reticulum Ca2+-ATPase 2b Regulation via Transmembrane Helix Interplay.
Authors: Inoue, M. / Sakuta, N. / Watanabe, S. / Zhang, Y. / Yoshikaie, K. / Tanaka, Y. / Ushioda, R. / Kato, Y. / Takagi, J. / Tsukazaki, T. / Nagata, K. / Inaba, K.
History
DepositionMay 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)118,3755
Polymers117,7651
Non-polymers6104
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-25 kcal/mol
Surface area43470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.079, 84.053, 118.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1027-

ILE

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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: 117764.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2A2, ATP2B / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P16615, EC: 3.6.3.8
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 28-34% polyethylene glycol 250 dimethylethanol, 100 mM tris(hydroxymethyl)aminomethane 100 mM potassium thiocyanate
PH range: 7.1-7.3

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL32XU11
SYNCHROTRONSPring-8 BL32XU21
SYNCHROTRONSPring-8 BL32XU31
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELJun 15, 2016
DECTRIS EIGER X 16M2PIXELJul 9, 2016
DECTRIS EIGER X 16M3PIXELOct 4, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
31
ReflectionResolution: 3.45→48.222 Å / Num. obs: 21039 / % possible obs: 93.7 % / Redundancy: 8.9 % / CC1/2: 0.963 / Net I/σ(I): 4.7
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.511 / % possible all: 77

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5S

1t5s


Resolution: 3.45→48.222 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3075 1006 4.82 %
Rwork0.2463 --
obs0.2493 20856 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→48.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7466 0 34 0 7500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077638
X-RAY DIFFRACTIONf_angle_d0.72610348
X-RAY DIFFRACTIONf_dihedral_angle_d3.7264619
X-RAY DIFFRACTIONf_chiral_restr0.0461229
X-RAY DIFFRACTIONf_plane_restr0.0051305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4501-3.6320.3418900.28012197X-RAY DIFFRACTION72
3.632-3.85940.36351280.272616X-RAY DIFFRACTION87
3.8594-4.15730.30921600.25472869X-RAY DIFFRACTION97
4.1573-4.57540.33141360.25572965X-RAY DIFFRACTION97
4.5754-5.23670.31921730.23052981X-RAY DIFFRACTION99
5.2367-6.5950.31251530.26373046X-RAY DIFFRACTION99
6.595-48.22630.26711660.22413176X-RAY DIFFRACTION99

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