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- PDB-5xa7: Complete structure factors and an atomic model of the calcium pum... -

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Basic information

Entry
Database: PDB / ID: 5xa7
TitleComplete structure factors and an atomic model of the calcium pump (SERCA1A) and associated phospholipids in the E1-2CA2+ crystals
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / P-TYPE ATPASE / CALCIUM TRANSPORT / CALCIUM BINDING / ENDOPLASMIC RETICULUM / SARCOPLASMIC RETICULUM / MET 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 / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative 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 / regulation of striated muscle contraction / calcium ion import into sarcoplasmic reticulum / negative 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 / 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 / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / haloacid dehalogenase-like hydrolase / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / HAD superfamily/HAD-like / 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 / Distorted Sandwich / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / 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: 3.2 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 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)136,49438
Polymers109,6291
Non-polymers26,86537
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-54 kcal/mol
Surface area58220 Å2
Unit cell
Length a, b, c (Å)166.200, 64.545, 146.220
Angle α, β, γ (deg.)90.00, 98.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 34 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM 2 OF DATABASE UNP P04191. THE C-TERMINAL RESIDUES IN ...SEQUENCE OF THE PROTEIN WAS BASED ON ISOFORM 2 OF DATABASE UNP P04191. THE C-TERMINAL RESIDUES IN P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, THERE IS ONLY ONE C-TERMINAL RESIDUE 994 GLY.

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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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 283 K / Method: microdialysis / pH: 6.1 / Details: PEG 2000

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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→144.75 Å / Num. obs: 25724 / % possible obs: 100 % / Redundancy: 1 % / Net I/σ(I): 81.76

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Processing

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

1wpe
PDB Unreleased entry


Resolution: 3.2→82.27 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0.58 / Phase error: 24.19
RfactorNum. reflection% reflection
Rfree0.2439 1231 4.79 %
Rwork0.2254 --
obs0.2263 25709 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→82.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7674 0 751 117 8542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028531
X-RAY DIFFRACTIONf_angle_d0.5511584
X-RAY DIFFRACTIONf_dihedral_angle_d11.6363072
X-RAY DIFFRACTIONf_chiral_restr0.0211269
X-RAY DIFFRACTIONf_plane_restr0.0031426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.32810.31771310.27622664X-RAY DIFFRACTION100
3.3281-3.47960.31291310.26272705X-RAY DIFFRACTION100
3.4796-3.6630.29051420.2472687X-RAY DIFFRACTION100
3.663-3.89250.25431320.24052723X-RAY DIFFRACTION100
3.8925-4.19310.24811410.2172694X-RAY DIFFRACTION100
4.1931-4.6150.20941340.20262724X-RAY DIFFRACTION100
4.615-5.28270.21691440.20352717X-RAY DIFFRACTION100
5.2827-6.65520.25391280.2262747X-RAY DIFFRACTION100
6.6552-82.2940.20381480.21452817X-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)
10.03220.16250.0542-0.302-0.37330.3851-0.18790.08040.14780.0010.1746-0.14580.17710.2739-0.00870.37210.0599-0.00940.5612-0.20860.528869.429419.457432.5455
22.3398-0.9024-0.75352.76180.79031.43610.1251-0.1497-0.03370.1091-0.0457-0.2107-0.1989-0.0146-0.02980.37860.00310.03710.1538-0.00120.370734.092159.130355.3969
32.4706-0.3935-1.35151.76180.83531.00780.07151.14530.1965-0.2136-0.02630.0588-0.1827-0.68110.24180.24080.0352-0.10560.6519-0.00650.215449.361119.629116.4633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 373 )
2X-RAY DIFFRACTION2chain 'A' and (resid 374 through 601 )
3X-RAY DIFFRACTION3chain 'A' and (resid 602 through 994 )

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