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- PDB-4ycn: Crystal structure of the calcium pump with bound marine macrolide BLLB -

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Basic information

Entry
Database: PDB / ID: 4ycn
TitleCrystal structure of the calcium pump with bound marine macrolide BLLB
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / Ca2+ / ion pump
Function / homology
Function and homology information


positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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 / H zone / positive regulation of fast-twitch skeletal muscle fiber contraction / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / 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
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 / haloacid dehalogenase-like hydrolase / 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-7BL / PHOSPHATIDYLETHANOLAMINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsMorita, M. / Ogawa, H. / Ohno, O. / Yamori, T. / Suenaga, K. / Toyoshima, C.
CitationJournal: Febs Lett. / Year: 2015
Title: Biselyngbyasides, cytotoxic marine macrolides, are novel and potent inhibitors of the Ca(2+) pumps with a unique mode of binding
Authors: Morita, M. / Ogawa, H. / Ohno, O. / Yamori, T. / Suenaga, K. / Toyoshima, C.
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)111,7567
Polymers109,6451
Non-polymers2,1126
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-39 kcal/mol
Surface area45930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.540, 71.540, 587.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 109644.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-7BL / (4S,5E,8S,9E,11S,13E,15E,18R)-4-hydroxy-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]oxacyclooctadeca-5,9,13,15-tetraen-2-one / biselyngbyolide B


Mass: 428.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H40O4
#5: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Sequence detailsThis sequence is Isoform SERCA1A (identifier: P04191-2).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.07% C12E8, 0.5 mg ml-1 phosphatidylcholine (PC), 1 mM MgCl2, 18% glycerol, 0.05 mM BLLB, and 2 mM EGTA, 10 mM MOPS, 10 mM MES, The reservoir consisted of 16% glycerol, 14% PEG3350, 1 mM ...Details: 0.07% C12E8, 0.5 mg ml-1 phosphatidylcholine (PC), 1 mM MgCl2, 18% glycerol, 0.05 mM BLLB, and 2 mM EGTA, 10 mM MOPS, 10 mM MES, The reservoir consisted of 16% glycerol, 14% PEG3350, 1 mM MgCl2, 200 mM MgSO4, 1 mM EGTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 206048 / % possible obs: 99.2 % / Redundancy: 14 % / Net I/σ(I): 15.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata scaling
SCALEPACKdata scaling
RefinementResolution: 3.5→15.997 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 3 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 624 3.2 %
Rwork0.2102 --
obs0.2114 19476 95.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→15.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 80 0 7754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017891
X-RAY DIFFRACTIONf_angle_d0.40610694
X-RAY DIFFRACTIONf_dihedral_angle_d10.2762925
X-RAY DIFFRACTIONf_chiral_restr0.0181243
X-RAY DIFFRACTIONf_plane_restr0.0021361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5003-3.84820.31591410.25644079X-RAY DIFFRACTION85
3.8482-4.39490.25411780.22084711X-RAY DIFFRACTION98
4.3949-5.49940.23491490.21084904X-RAY DIFFRACTION99
5.4994-15.9970.22571560.18925158X-RAY DIFFRACTION99
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)
10.7469-0.68391.61040.5447-1.28682.8931-0.2184-0.57510.14380.2188-0.00410.0933-0.1323-0.65840.35860.64860.0813-0.04721.19350.01540.721910.6842-12.118946.984
22.0420.48370.40233.0775-0.13882.961-0.0067-0.00360.4233-0.31440.2834-0.0691-0.3928-0.0530.03560.49090.056-0.10380.26320.04290.63236.5432-1.504216.3832
30.5597-0.35661.04780.679-0.18061.5056-0.0026-0.2348-0.05440.31280.18450.1622-0.18-0.2098-0.01180.51760.019-0.04230.55660.08760.543328.3936-15.449746.0033
44.0107-0.35790.25782.49880.27572.697-0.30870.00270.52840.05550.21020.1148-0.28480.22130.00270.4773-0.164-0.10760.54760.23370.688436.83778.67551.0133
50.9590.08830.18770.5989-0.83333.50460.1273-0.08840.01170.0152-0.17190.00740.30350.44040.01550.46940.0252-0.11830.51880.08630.577536.6075-12.563132.0136
61.26220.40120.98251.7083-0.73281.76470.1679-0.756-0.08230.5866-0.0243-0.0591-0.25770.5046-0.08551.0983-0.0486-0.17151.56310.10670.722946.8134-17.191479.4019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 201 )
3X-RAY DIFFRACTION3chain 'A' and (resid 202 through 373 )
4X-RAY DIFFRACTION4chain 'A' and (resid 374 through 554 )
5X-RAY DIFFRACTION5chain 'A' and (resid 555 through 831 )
6X-RAY DIFFRACTION6chain 'A' and (resid 832 through 994 )

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