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- PDB-5xa9: Complete structure factors and an atomic model of the calcium pum... -

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Basic information

Entry
Database: PDB / ID: 5xa9
TitleComplete structure factors and an atomic model of the calcium pump (SERCA1A) and associated phospholipids in the E2-ALF-(TG) crystals of C2 symmetry
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / P-TYPE ATPASE / CALCIUM TRANSPORT / CALCIUM BINDING / ATP BINDING / ENDOPLASMIC RETICULUM / SARCOPLASMIC RETICULUM / METAL TRANSPORT
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 / regulation of striated muscle contraction / negative 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 / regulation of striated muscle contraction / negative 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 / 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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / 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
TETRAFLUOROALUMINATE ION / 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: 3.2 Å
AuthorsNorimatsu, Y. / Hasegawa, K. / Shimizu, N. / Toyoshima, C.
CitationJournal: Nature / Year: 2017
Title: Protein-phospholipid interplay revealed with crystals of a calcium pump.
Authors: Norimatsu, Y. / Hasegawa, K. / Shimizu, N. / Toyoshima, C.
History
DepositionMar 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,16938
Polymers109,6291
Non-polymers27,54037
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-82 kcal/mol
Surface area55170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.400, 70.100, 141.900
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 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: 109628.617 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

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Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#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 / Thapsigargin


Mass: 650.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50O12 / Comment: inhibitor*YM
#5: 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.: 34 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 283 K / Method: microdialysis / pH: 6.1 / Details: PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 13, 2005
RadiationMonochromator: ROTATED-INCLINED DOUBLE- CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 3.2→135.7 Å / Num. obs: 27887 / % possible obs: 100 % / Redundancy: 1 % / Net I/σ(I): 49.78

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WPE

1wpe
PDB Unreleased entry


Resolution: 3.2→135.7 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.38
RfactorNum. reflection% reflection
Rfree0.235 1376 4.94 %
Rwork0.215 --
obs0.216 27842 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→135.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 800 197 8671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028707
X-RAY DIFFRACTIONf_angle_d0.86511836
X-RAY DIFFRACTIONf_dihedral_angle_d9.8553116
X-RAY DIFFRACTIONf_chiral_restr0.0911283
X-RAY DIFFRACTIONf_plane_restr0.0031444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31440.32991290.27312604X-RAY DIFFRACTION100
3.3144-3.44710.32611480.24622625X-RAY DIFFRACTION100
3.4471-3.6040.28061320.2392625X-RAY DIFFRACTION100
3.604-3.7940.29381520.2382611X-RAY DIFFRACTION100
3.794-4.03170.28281420.22012635X-RAY DIFFRACTION100
4.0317-4.3430.22141540.20222636X-RAY DIFFRACTION100
4.343-4.780.19581270.17832654X-RAY DIFFRACTION100
4.78-5.47160.22161280.2042654X-RAY DIFFRACTION100
5.4716-6.89310.26321320.23772672X-RAY DIFFRACTION100
6.8931-84.76290.19161320.212750X-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)
10.22390.0863-0.31271.25711.2242.0569-0.18810.2879-0.83820.71320.2437-0.46941.33-0.16370.02520.885-0.0650.04640.6085-0.11330.969635.754344.3257116.5549
20.2503-0.07270.17251.9735-0.050.11280.0107-0.2464-0.0391-0.768-0.26880.8556-0.10851.3152-0.22211.6892-0.05560.10972.37090.29431.248217.952959.768167.7352
31.9125-2.10940.8712.1243-0.45331.3602-0.11690.2020.1380.0138-0.0913-0.69140.5385-0.0968-0.03510.6715-0.07270.04540.4399-0.03590.826932.873556.334118.6124
40.36830.20371.86340.52941.08773.2484-0.1709-0.01180.259-0.16090.12190.1575-0.7086-0.35981.13290.5279-0.13030.03060.94470.20310.576411.860372.2744100.4674
53.3744-0.7854-1.35350.65460.68166.2143-0.3826-0.181-0.1989-0.06280.0832-0.2721-0.3089-0.1025-0.00450.79490.04040.0110.6247-0.03470.948331.289481.3888140.2257
60.84530.11590.71260.29550.81022.6848-0.24890.29280.1099-0.2513-0.05830.1287-0.199-0.9399-0.12280.7791-0.18690.02791.08060.05460.71216.052469.317293.965
70.8045-0.16320.86160.0033-0.18550.9646-0.13220.5976-0.32980.0393-0.3006-0.26680.0450.5042-0.09331.2363-0.1232-0.34171.74290.18650.96-0.757480.992967.5424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 51 THROUGH 107 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 108 THROUGH 247 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 248 THROUGH 419 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 420 THROUGH 580 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 581 THROUGH 893 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 894 THROUGH 994 )

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