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- PDB-3w5a: Crystal structure of the calcium pump and sarcolipin from rabbit ... -

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Basic information

Entry
Database: PDB / ID: 3w5a
TitleCrystal structure of the calcium pump and sarcolipin from rabbit fast twitch skeletal muscle in the E1.Mg2+ state
Components
  • SERCA1a
  • Sarcolipin
KeywordsMETAL TRANSPORT/MEMBRANE PROTEIN / P-TYPE ATPASE / HYDROLASE / CALCIUM TRANSPORT / CALCIUM BINDING / ATP BINDING / ENDOPLASMIC RETICULUM / SARCOLIPIN / METAL TRANSPORT-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


positive regulation of protein depolymerization / regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of relaxation of muscle / negative regulation of protein-containing complex disassembly / negative regulation of calcium ion transmembrane transporter activity / positive regulation of cardiac muscle cell contraction / positive regulation of calcium ion import into sarcoplasmic reticulum / H zone ...positive regulation of protein depolymerization / regulation of ATPase-coupled calcium transmembrane transporter activity / negative regulation of calcium ion binding / negative regulation of ATPase-coupled calcium transmembrane transporter activity / regulation of relaxation of muscle / negative regulation of protein-containing complex disassembly / negative regulation of calcium ion transmembrane 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 / negative regulation of calcium ion import / calcium ion import into sarcoplasmic reticulum / negative regulation of striated muscle contraction / regulation of striated muscle contraction / positive regulation of ATPase-coupled calcium transmembrane transporter activity / P-type Ca2+ transporter / sarcoplasmic reticulum calcium ion transport / negative regulation of catalytic activity / P-type calcium transporter activity / I band / enzyme inhibitor activity / regulation of calcium ion transport / endoplasmic reticulum-Golgi intermediate compartment / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / intracellular calcium ion homeostasis / calcium ion transport / ATPase binding / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
Similarity search - Function
Sarcolipin / Sarcolipin / 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 ...Sarcolipin / Sarcolipin / 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
PHOSPHATIDYLETHANOLAMINE / Chem-TM1 / Calcium-transporting ATPase / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / Sarcolipin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsToyoshima, C. / Iwasawa, S. / Ogawa, H. / Hirata, A. / Tsueda, J. / Inesi, G.
CitationJournal: Nature / Year: 2013
Title: Crystal structures of the calcium pump and sarcolipin in the Mg2+-bound E1 state.
Authors: Toyoshima, C. / Iwasawa, S. / Ogawa, H. / Hirata, A. / Tsueda, J. / Inesi, G.
History
DepositionJan 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERCA1a
B: SERCA1a
C: Sarcolipin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,96416
Polymers223,0343
Non-polymers4,93013
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)352.883, 55.729, 187.951
Angle α, β, γ (deg.)90.00, 119.02, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9946, 0.031613, -0.098853), (0.0315, 0.9995, 0.002698), (0.098889, -0.000431, -0.995098)214.39124, -32.56528, 69.97948

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein SERCA1a / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1


Mass: 109628.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B6CAM1, UniProt: P04191*PLUS
#2: Protein/peptide Sarcolipin


Mass: 3776.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P42532

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Non-polymers , 5 types, 25 molecules

#3: Chemical ChemComp-TM1 / 2',3'-O-[(1r)-2,4,6-trinitrocyclohexa-2,5-diene-1,1-diyl]adenosine 5'-(dihydrogen phosphate)


Mass: 558.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N8O13P
#4: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.05 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 64852 / Num. obs: 61685 / % possible obs: 95.1 % / Observed criterion σ(I): 2.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.4 % / Rsym value: 0.412 / % possible all: 79.3

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Processing

Software
NameVersionClassification
BSSdata collection
CNSrefinement
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→15 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.889 / SU B: 23.856 / SU ML: 0.406 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28307 3113 5 %RANDOM
Rwork0.24764 ---
all0.24945 ---
obs0.24945 58572 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.777 Å2
Baniso -1Baniso -2Baniso -3
1-2.89 Å20 Å23.98 Å2
2---0.41 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 3.01→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15613 0 177 12 15802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916077
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.98521817
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54152016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.6224.299649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.239152815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4891599
X-RAY DIFFRACTIONr_chiral_restr0.0720.22532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111866
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.006→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 180 -
Rwork0.396 3211 -
obs--76.07 %

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