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- PDB-7bt2: Crystal structure of the SERCA2a in the E2.ATP state -

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Basic information

Entry
Database: PDB / ID: 7bt2
TitleCrystal structure of the SERCA2a in the E2.ATP state
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 2
KeywordsHYDROLASE / P-type ATPase / Ca2+-ATPase
Function / homology
Function and homology information


longitudinal sarcoplasmic reticulum / ER-nucleus signaling pathway / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential ...longitudinal sarcoplasmic reticulum / ER-nucleus signaling pathway / P-type calcium transporter activity involved in regulation of cardiac muscle cell membrane potential / regulation of calcium ion-dependent exocytosis of neurotransmitter / calcium ion transport from cytosol to endoplasmic reticulum / positive regulation of endoplasmic reticulum calcium ion concentration / calcium ion-transporting ATPase complex / T-tubule organization / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cardiac muscle cell membrane potential / ribbon synapse / platelet dense tubular network membrane / calcium ion import into sarcoplasmic reticulum / Pre-NOTCH Processing in Golgi / P-type Ca2+ transporter / sarcoplasmic reticulum calcium ion transport / negative regulation of heart contraction / transition between fast and slow fiber / P-type calcium transporter activity / regulation of the force of heart contraction / cardiac muscle hypertrophy in response to stress / endoplasmic reticulum calcium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / S100 protein binding / lncRNA binding / relaxation of cardiac muscle / Reduction of cytosolic Ca++ levels / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of heart rate / positive regulation of cardiac muscle cell apoptotic process / Ion transport by P-type ATPases / autophagosome assembly / regulation of cardiac conduction / epidermis development / Ion homeostasis / monoatomic ion transmembrane transport / sarcoplasmic reticulum membrane / response to endoplasmic reticulum stress / sarcoplasmic reticulum / negative regulation of receptor binding / calcium ion transmembrane transport / intracellular calcium ion homeostasis / neuron cellular homeostasis / cellular response to oxidative stress / transmembrane transporter binding / cell adhesion / calcium ion binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / plasma 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
ADENOSINE-5'-TRIPHOSPHATE / : / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.00002849524 Å
AuthorsKabashima, Y. / Ogawa, H. / Nakajima, R. / Toyoshima, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: What ATP binding does to the Ca2+pump and how nonproductive phosphoryl transfer is prevented in the absence of Ca2.
Authors: Kabashima, Y. / Ogawa, H. / Nakajima, R. / Toyoshima, C.
History
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6158
Polymers109,8021
Non-polymers3,8137
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-8 kcal/mol
Surface area48140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.604, 270.382, 97.34
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,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 2 / SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum type / ...SR Ca(2+)-ATPase 2 / Calcium pump 2 / Calcium-transporting ATPase sarcoplasmic reticulum type / slow twitch skeletal muscle isoform / Endoplasmic reticulum class 1/2 Ca(2+) ATPase


Mass: 109801.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATP2A2, ATP2B / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: P16615, P-type Ca2+ transporter

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Non-polymers , 5 types, 109 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#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.: 4 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 5% glycerol, 20-23% PEG1500, 5 mM MgSO4, 6 mM EGTA, 6% 2-methyl-2,4-pentanediol (MPD) and 100 mM MOPS pH 7.2
PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 40 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 48563 / % possible obs: 97.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 65.0535037813 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.103 / Χ2: 1.069 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3559 / CC1/2: 0.577 / CC star: 0.856 / Rrim(I) all: 0.98 / Χ2: 1.076 / % possible all: 88.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIX1.9_1692refinement
SCALEPACKdata scaling
CNSphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AR4

3ar4


Resolution: 3.00002849524→14.9879317255 Å / SU ML: 0.306748451204 / Cross valid method: FREE R-VALUE / σ(F): 2.00125865324 / Phase error: 21.1949287348
Details: refined at 2.6 angstrom resolution using full reflection data
RfactorNum. reflection% reflection
Rfree0.222002563214 1568 5 %
Rwork0.192444544089 --
obs0.193939305416 31360 97.1288753988 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 117 Å2
Refinement stepCycle: LAST / Resolution: 3.00002849524→14.9879317255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 128 102 7869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006482576712437902
X-RAY DIFFRACTIONf_angle_d1.1074216301310730
X-RAY DIFFRACTIONf_chiral_restr0.3026799074661258
X-RAY DIFFRACTIONf_plane_restr0.005824230788481359
X-RAY DIFFRACTIONf_dihedral_angle_d12.40998059542929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.00002849524-3.0960.251897240911480.2222840473792623X-RAY DIFFRACTION95.8823529412
3.096-3.20570.2497025829081420.2205654545492652X-RAY DIFFRACTION96.046751461
3.2057-3.33270.2820328508671340.2078649178632715X-RAY DIFFRACTION98.0048159615
3.3327-3.48250.2647489017011380.2030096257042708X-RAY DIFFRACTION97.767090347
3.4825-3.66360.2103053313861370.1968990970982680X-RAY DIFFRACTION97.6429809359
3.6636-3.88940.2247741008761430.1916365368532737X-RAY DIFFRACTION97.9258755525
3.8894-4.18360.2191827855251470.1782939850792677X-RAY DIFFRACTION97.4129010003
4.1836-4.59360.1756895464531430.1684955925962747X-RAY DIFFRACTION98.0325644505
4.5936-5.23340.2084856898361510.1835433267732728X-RAY DIFFRACTION97.560149102
5.2334-6.50260.2654892328161470.2216347284492735X-RAY DIFFRACTION96.5494137353
6.5026-14.98793172550.2024123700231380.1827962092822790X-RAY DIFFRACTION95.6862745098
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)
10.303216466580.0972632621534-0.09248075596070.0351694352846-0.010193659080.127508873317-0.127558012442-0.3431229779660.09851208326890.0129354599155-0.175432143162-0.116257932252-0.1964547860570.0477274937808-0.3246483186750.5969630972360.0724651604693-0.4292673951330.603894439240.03487087269370.616829286549-18.5612454858-32.7777892446-6.9719019738
20.0128283296133-0.001826304841860.004725847225090.00116656336505-0.00365455120220.003766841850960.0155423176190.00967348254175-0.0790834005935-0.007135832606790.05655230792450.03097321885310.002111082918380.03877707870131.03857620514E-61.05824400645-0.308516248571-0.002132119020690.7060247473670.3227346104271.32931734729-15.88883540911.01465545579-38.613515288
30.4422045918210.0894490730623-0.01252264497070.393208830572-0.3095403887340.675957815474-0.138590582723-0.03974157602760.1562687420.07586815850270.0110868121376-0.184004545317-0.237789645274-0.225443718324-0.1751332512420.2312212828850.0726847264633-0.08369706387990.148780317164-0.004753527854040.231084856063-41.0328028606-37.8495777224-23.7348028696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 247 )
2X-RAY DIFFRACTION2chain 'A' and (resid 248 through 310 )
3X-RAY DIFFRACTION3chain 'A' and (resid 311 through 991 )

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