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- PDB-6yaa: Structure of the (SR) Ca2+-ATPase bound to the inhibitor compound... -

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Basic information

Entry
Database: PDB / ID: 6yaa
TitleStructure of the (SR) Ca2+-ATPase bound to the inhibitor compound CAD204520 and TNP-ATP
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / P-TYPE ATPASE / INHIBITORY COMPLEX / CALCIUM-TRANSPORTING ATPASE
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity ...positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / positive regulation of ATPase-coupled calcium transmembrane transporter activity / positive regulation of fast-twitch skeletal muscle fiber contraction / H zone / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / P-type Ca2+ transporter / P-type calcium transporter activity / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / intracellular calcium ion homeostasis / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / 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
Chem-128 / : / Chem-OHW / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHeit, S. / Marchesini, M. / Gherli, A. / Montanaro, A. / Patrizi, L. / Sorrentino, C. / Pagliaro, L. / Rompietti, C. / Kitara, S. / Olesen, C.E. ...Heit, S. / Marchesini, M. / Gherli, A. / Montanaro, A. / Patrizi, L. / Sorrentino, C. / Pagliaro, L. / Rompietti, C. / Kitara, S. / Olesen, C.E. / Moller, J.V. / Savi, M. / Bocchi, L. / Vilella, R. / Rizzi, F. / Baglione, M. / Rastelli, G. / Loiacona, C. / La Starza, R. / Mecucci, C. / Stegmair, K. / Aversa, F. / Stilli, D. / Lund Winther, A.M. / Sportoletti, P. / Dalby-Brown, W. / Roti, G. / Bublitz, M.
CitationJournal: Cell Chem Biol / Year: 2020
Title: Blockade of Oncogenic NOTCH1 with the SERCA Inhibitor CAD204520 in T Cell Acute Lymphoblastic Leukemia.
Authors: Marchesini, M. / Gherli, A. / Montanaro, A. / Patrizi, L. / Sorrentino, C. / Pagliaro, L. / Rompietti, C. / Kitara, S. / Heit, S. / Olesen, C.E. / Moller, J.V. / Savi, M. / Bocchi, L. / ...Authors: Marchesini, M. / Gherli, A. / Montanaro, A. / Patrizi, L. / Sorrentino, C. / Pagliaro, L. / Rompietti, C. / Kitara, S. / Heit, S. / Olesen, C.E. / Moller, J.V. / Savi, M. / Bocchi, L. / Vilella, R. / Rizzi, F. / Baglione, M. / Rastelli, G. / Loiacono, C. / La Starza, R. / Mecucci, C. / Stegmaier, K. / Aversa, F. / Stilli, D. / Lund Winther, A.M. / Sportoletti, P. / Bublitz, M. / Dalby-Brown, W. / Roti, G.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 24, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7994
Polymers109,6031
Non-polymers1,1973
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-0 kcal/mol
Surface area45390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.632, 71.632, 588.306
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 109602.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: HIND LEG MUSCLE / References: UniProt: P04191, P-type Ca2+ transporter
#2: Chemical ChemComp-128 / SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE


Type: RNA linking / Mass: 718.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N8O19P3
#3: Chemical ChemComp-OHW / 4-[2-[(2~{R})-2-[3-propyl-6-(trifluoromethyloxy)-1~{H}-indol-2-yl]piperidin-1-yl]ethyl]morpholine / CAD204520


Mass: 439.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H32F3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
Has ligand of interestY
Has protein modificationY

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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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% glycerol, 14% PEG6000, 100 mM NaCl and 6% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.4→58.83 Å / Num. obs: 22672 / % possible obs: 100 % / Redundancy: 36.6 % / CC1/2: 1 / Rpim(I) all: 0.077 / Net I/σ(I): 9.3
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 32.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4468 / CC1/2: 0.652 / Rpim(I) all: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXv1.17.1refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uu0

4uu0


Resolution: 3.4→57.84 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2554 1138 5.05 %
Rwork0.2281 --
obs0.2295 22530 99.95 %
Displacement parametersBiso mean: 118.33 Å2
Refinement stepCycle: LAST / Resolution: 3.4→57.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 78 0 7749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287896
X-RAY DIFFRACTIONf_angle_d0.7210722
X-RAY DIFFRACTIONf_chiral_restr0.04331237
X-RAY DIFFRACTIONf_plane_restr0.0051364
X-RAY DIFFRACTIONf_dihedral_angle_d16.16952937

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