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- PDB-5zmw: Crystal structure of the E309Q mutant of SR Ca2+-ATPase in E2(TG) -

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Basic information

Entry
Database: PDB / ID: 5zmw
TitleCrystal structure of the E309Q mutant of SR Ca2+-ATPase in E2(TG)
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / ATP-BINDING / CALCIUM TRANSPORT / ENDOPLASMIC RETICULUM / ION TRANSPORT / MAGNESIUM / METAL-BINDING / NUCLEOTIDE-BINDING / PHOSPHORYLATION / SARCOPLASMIC RETICULUM / TRANSMEMBRANE / TRANSPORT
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
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-TG1 / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOgawa, H. / Hirata, A. / Tsueda, J. / Toyoshima, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanism of the E2 to E1 transition in Ca2+pump revealed by crystal structures of gating residue mutants.
Authors: Tsunekawa, N. / Ogawa, H. / Tsueda, J. / Akiba, T. / Toyoshima, C.
History
DepositionApr 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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)111,9086
Polymers110,1731
Non-polymers1,7355
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-46 kcal/mol
Surface area47710 Å2
Unit cell
Length a, b, c (Å)260.977, 86.895, 60.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 3 molecules A

#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: 110173.172 Da / Num. of mol.: 1 / Mutation: E309Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ATP2A1 / Cell (production host): COS-7 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: P04191, EC: 3.6.3.8
#5: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 4 types, 239 molecules

#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.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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 / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSequence of the protein was based on isoform SERCA1A (P04191-2) of database AT2A1_RABIT.

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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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 16% glycerol, 16-18% PEG2000, 2.5 mM NaN3, 1 mM MgSO4, 1 mM EGTA, 0.15% decylmaltoside and 40 mM MES, pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→16 Å / Num. obs: 47627 / % possible obs: 98.75 % / Redundancy: 9 % / Net I/σ(I): 18.1
Reflection shellResolution: 2.5→2.58 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3311: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15.928 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 1480 3.11 %
Rwork0.2222 --
obs0.2234 47627 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→15.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7711 0 118 236 8065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037977
X-RAY DIFFRACTIONf_angle_d0.53210826
X-RAY DIFFRACTIONf_dihedral_angle_d11.9094814
X-RAY DIFFRACTIONf_chiral_restr0.041276
X-RAY DIFFRACTIONf_plane_restr0.0041370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58040.41171190.35824095X-RAY DIFFRACTION98
2.5804-2.67220.34621380.33464111X-RAY DIFFRACTION99
2.6722-2.77860.38881280.31544159X-RAY DIFFRACTION99
2.7786-2.90440.3691240.30444157X-RAY DIFFRACTION98
2.9044-3.05650.34231330.27414139X-RAY DIFFRACTION99
3.0565-3.24650.2851310.25624185X-RAY DIFFRACTION99
3.2465-3.49470.31681330.2264226X-RAY DIFFRACTION100
3.4947-3.84190.24081530.20494209X-RAY DIFFRACTION99
3.8419-4.38760.20231290.17394229X-RAY DIFFRACTION99
4.3876-5.49010.17831500.1674243X-RAY DIFFRACTION98
5.4901-15.92810.20621420.17584394X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 166.3239 Å / Origin y: 33.735 Å / Origin z: 3.5489 Å
111213212223313233
T0.1065 Å20.0224 Å20.0847 Å2-0.1183 Å20.0635 Å2--0.0271 Å2
L0.4534 °2-0.3056 °2-0.0405 °2-0.6499 °20.1542 °2--0.1564 °2
S-0.195 Å °-0.0283 Å °-0.1331 Å °0.0428 Å °0.2015 Å °0.097 Å °-0.016 Å °-0.0771 Å °-0.0187 Å °
Refinement TLS groupSelection details: all

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