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- PDB-4nab: Structure of the (SR)Ca2+-ATPase mutant E309Q in the Ca2-E1-MgAMP... -

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Basic information

Entry
Database: PDB / ID: 4nab
TitleStructure of the (SR)Ca2+-ATPase mutant E309Q in the Ca2-E1-MgAMPPCP form
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Mutant E309Q / P-type ATPase / Calcium-transporting ATPase / Sarcoplasmic reticulum
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 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 ...Calcium-transporting ATPase, transmembrane domain / Calcium-transporting ATPase, transmembrane domain / P-type ATPase, subfamily IIA, SERCA-type / 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 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBublitz, M. / Clausen, J.D. / Arnou, B. / Montigny, C. / Jaxel, C. / Nissen, P. / Moller, J.V. / Andersen, J.P. / le Maire, M.
CitationJournal: Embo J. / Year: 2013
Title: SERCA mutant E309Q binds two Ca(2+) ions but adopts a catalytically incompetent conformation.
Authors: Clausen, J.D. / Bublitz, M. / Arnou, B. / Montigny, C. / Jaxel, C. / Moller, J.V. / Nissen, P. / Andersen, J.P. / le Maire, M.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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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)111,0895
Polymers110,1821
Non-polymers9064
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.010, 55.790, 161.790
Angle α, β, γ (deg.)90.00, 109.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: 110182.305 Da / Num. of mol.: 1 / Mutation: E309Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ATP2A1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: 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.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITED SEQUENCE CORRESPONDS TO ISOFORM SERCA1A OF THE UNIPROT ENTRY P04191.

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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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 293 K / pH: 6.8
Details: 5.5% PEG6K, 5 mM CaCl2, 15% glycerol, 27 mM MgCl2, 3% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97935
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.5→70 Å / Num. obs: 18252 / % possible obs: 99.9 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.6 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
remdaq.pilatusdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→67.007 Å / SU ML: 0.5 / σ(F): 2 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 920 5.07 %
Rwork0.2163 --
obs0.2185 18161 99.91 %
all-18161 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→67.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 57 2 6486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036605
X-RAY DIFFRACTIONf_angle_d0.6728949
X-RAY DIFFRACTIONf_dihedral_angle_d12.9342465
X-RAY DIFFRACTIONf_chiral_restr0.0451036
X-RAY DIFFRACTIONf_plane_restr0.0041136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4999-3.68440.32861200.26742444X-RAY DIFFRACTION100
3.6844-3.91520.30371320.23852397X-RAY DIFFRACTION100
3.9152-4.21740.29031450.2122449X-RAY DIFFRACTION100
4.2174-4.64170.26051300.18412476X-RAY DIFFRACTION100
4.6417-5.31320.26211250.19192417X-RAY DIFFRACTION100
5.3132-6.69310.28861310.25352490X-RAY DIFFRACTION100
6.6931-67.01950.23741370.21162568X-RAY DIFFRACTION100
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)
14.5602-0.71481.09925.4573-1.1050.42150.2252-0.72320.52490.92570.0320.1129-0.72740.5532-0.43780.7144-0.2232-0.05421.2082-0.12530.6834-7.5121-14.21777.3059
21.3552-0.9104-0.51365.13412.08342.9422-0.1912-0.39670.1680.75910.48380.42210.43010.6796-0.3750.4329-0.08740.04910.92910.03020.5797-19.3378-20.238310.8352
35.3141-0.7937-6.04714.96893.01699.5998-0.2139-0.3499-0.39630.59320.0230.28850.13030.16330.16851.04170.1146-0.1220.67460.09860.6023-40.2004-6.808746.9463
45.4721.05250.1955.56351.00490.16630.3037-0.90120.08960.3089-0.2285-0.0912-0.8468-0.47050.00962.07950.11930.00861.2552-0.09930.7113-43.777813.7671.2887
52.34380.0814-0.30243.4576-0.59535.347-0.10030.2197-0.0792-0.07710.0511-0.0575-0.3865-0.33320.07330.4352-0.0333-0.11360.70640.02720.4847-28.8736-9.66780.1956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 47:122
2X-RAY DIFFRACTION2chain A and resseq 241:330
3X-RAY DIFFRACTION3chain A and (resseq 331:357 or resseq 604:750)
4X-RAY DIFFRACTION4chain A and resseq 358:603
5X-RAY DIFFRACTION5chain A and resseq 751:994

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