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- PDB-2eau: Crystal structure of the SR CA2+-ATPASE with bound CPA in the pre... -

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Basic information

Entry
Database: PDB / ID: 2eau
TitleCrystal structure of the SR CA2+-ATPASE with bound CPA in the presence of curcumin
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / MEMBRANE PROTEIN / P-TYPE ATPASE / HAD FOLD / Ca2+ / ion pump
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
Chem-CZA / PHOSPHATIDYLETHANOLAMINE / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakahashi, M. / Kondou, Y. / Toyoshima, C.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Interdomain communication in calcium pump as revealed in the crystal structures with transmembrane inhibitors
Authors: Takahashi, M. / Kondou, Y. / Toyoshima, C.
#1: Journal: Nature / Year: 2000
Title: Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
Authors: Toyoshima, C. / Nakasako, M. / Nomura, H. / Ogawa, H.
#2: Journal: Nature / Year: 2002
Title: Structural changes in the calcium pump accompanying the dissociation of calcium
Authors: Toyoshima, C. / Nomura, H.
#3: Journal: Nature / Year: 2004
Title: Crystal structure of the calcium pump with a bound ATP analogue
Authors: Toyoshima, C. / Mizutani, T.
#4: Journal: Nature / Year: 2004
Title: Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
Authors: Toyoshima, C. / Nomura, H. / Tsuda, T.
#5: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural role of countertransport revealed in Ca(2+) pump crystal structure in the absence of Ca(2+)
Authors: Obara, K. / Miyashita, N. / Xu, C. / Toyoshima, I. / Sugita, Y. / Inesi, G. / Toyoshima, C.
History
DepositionFeb 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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)112,1675
Polymers109,6291
Non-polymers2,5394
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.648, 71.648, 586.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Calcium pump 1 / SERCA1 / SR Ca(2+)-ATPase 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...Calcium pump 1 / SERCA1 / SR Ca(2+)-ATPase 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) / Tissue: SKELETAL MUSCLE (WHITE) / References: UniProt: P04191, EC: 3.6.3.8
#2: Chemical ChemComp-CZA / (6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE


Mass: 336.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O3
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has protein modificationY
Nonpolymer detailsTHE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; ...THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;I=INSERTION CODE): M RES CSSEQI ATOMS PTY 1011 C12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 C28 C29 C32 C33 C34 C35 C36 C37 C38 C39 C40 C41 C42 C43 C44 PTY 1012 C12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 C28 C29 C32 C33 C34 C35 C36 C37 C38 C39 C40 C41 C42 C43 C44 PTY 1013 C12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 C28 C29 C32 C33 C34 C35 C36 C37 C38 C39 C40 C41 C42 C43 C44
Sequence detailsTHE C-TERMINAL RESIDUES IN UNP ENTRY P04191 ARE FROM 994 TO 1001, DPEDERRK. IN ISOFORM SERCA1A, ...THE C-TERMINAL RESIDUES IN UNP ENTRY 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: 2

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 283 K / Method: microdialysis / pH: 6.1 / Details: PEG 400, pH 6.1, MICRODIALYSIS, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 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: 2.8→20 Å / Num. all: 39533 / Num. obs: 39493 / % possible obs: 99.9 % / Observed criterion σ(F): 8.71 / Observed criterion σ(I): -1 / Redundancy: 17.1 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 32
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 7.2 / % possible all: 99.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IWO

1iwo


Resolution: 2.8→15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2718 1919 4.9 %RANDOM
Rwork0.2468 ---
all0.2474 39204 --
obs0.2468 38263 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.1879 Å2 / ksol: 0.3126 e/Å3
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.34 Å20 Å20 Å2
2---4.34 Å20 Å2
3---8.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7671 0 85 0 7756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it2.952
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.492.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 297 5.2 %
Rwork0.325 5466 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ligands.paramligands.top

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