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- PDB-27qy: Crystal structure of SR Ca2+-ATPase in E2(TG) with bound AHQ -

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Basic information

Entry
Database: PDB / ID: 27qy
TitleCrystal structure of SR Ca2+-ATPase in E2(TG) with bound AHQ
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsMEMBRANE PROTEIN / SR Ca+-ATPase / ion transport / TRANSPORT PROTEIN
Function / homology
Function and homology information


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 / positive regulation of cardiac muscle cell contraction / I band / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / 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 / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator 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 / P-type ATPase, cytoplasmic domain N / : / P-type ATPase actuator domain / 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
: / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-TG1 / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKanai, R. / Hirata, A. / Toyoshima, C. / Paula, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H02499 Japan
Japan Society for the Promotion of Science (JSPS)23H02443 Japan
Japan Society for the Promotion of Science (JSPS)24K01985 Japan
CitationJournal: J Membr Biol / Year: 2026
Title: Structural Basis of SERCA Inhibition by Derivatives of di-tert-butylhydroquinone Revealed by X-ray Crystallography.
Authors: Kanai, R. / Hirata, A. / Toyoshima, C. / Paula, S.
History
DepositionJun 9, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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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)117,03511
Polymers110,6011
Non-polymers6,43410
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-42 kcal/mol
Surface area45300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.499, 71.499, 590.485
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

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Protein , 1 types, 1 molecules A

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SERCA1 / SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...SERCA1 / 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: 110600.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P04191, P-type Ca2+ transporter

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Non-polymers , 5 types, 338 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-TG1 / OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER / THAPSIGARGIN


Mass: 650.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50O12
#4: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-A1MHM / 2,5-di-tert-amylhydroquinone / 2,5-bis(2-methylbutan-2-yl)benzene-1,4-diol


Mass: 250.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 283 K / Method: microdialysis / pH: 6.1
Details: 25% glycerol, 4% polyethylene glycol 400, 20 mM 2-(N-morpholino)ethanesulfonic acid-NaOH, 5 mM sodium azide, 0.2 mM dithiothreitol, 2ug/ml butylhydroxytoluene, 3 mM EGTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 76646 / % possible obs: 86.4 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.05 Å2 / CC1/2: 0.996 / Net I/σ(I): 10
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3833 / CC1/2: 0.339 / % possible all: 28.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AGV

2agv


Resolution: 2.12→14.99 Å / SU ML: 0.3001 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2629 2000 2.62 %
Rwork0.2217 74319 -
obs0.2228 76319 86.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.26 Å2
Refinement stepCycle: LAST / Resolution: 2.12→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 222 328 8221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098028
X-RAY DIFFRACTIONf_angle_d1.366610901
X-RAY DIFFRACTIONf_chiral_restr0.35341266
X-RAY DIFFRACTIONf_plane_restr0.01162373
X-RAY DIFFRACTIONf_dihedral_angle_d16.26793023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.180.4464160.3348613X-RAY DIFFRACTION10.17
2.18-2.240.3577690.33442553X-RAY DIFFRACTION42.11
2.24-2.30.35741150.33444262X-RAY DIFFRACTION70.56
2.3-2.380.33611410.30985225X-RAY DIFFRACTION87.17
2.38-2.460.31541550.29325801X-RAY DIFFRACTION95.02
2.46-2.560.30221630.27896007X-RAY DIFFRACTION99.6
2.56-2.670.32831620.27036058X-RAY DIFFRACTION99.86
2.67-2.810.28691640.25616093X-RAY DIFFRACTION99.94
2.81-2.990.31861660.24956142X-RAY DIFFRACTION99.95
2.99-3.220.26151640.23566117X-RAY DIFFRACTION99.94
3.22-3.540.27081670.22366194X-RAY DIFFRACTION100
3.54-4.040.24581680.20186246X-RAY DIFFRACTION100
4.04-5.060.22371710.1796353X-RAY DIFFRACTION100
5.06-14.990.22411790.18366655X-RAY DIFFRACTION99.99

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