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- PDB-3w5b: Crystal structure of the recombinant SERCA1a (calcium pump of fas... -

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Basic information

Entry
Database: PDB / ID: 3w5b
TitleCrystal structure of the recombinant SERCA1a (calcium pump of fast twitch skeletal muscle) in the E1.Mg2+ state
ComponentsSERCA1a
KeywordsMETAL TRANSPORT / P-TYPE ATPASE / HYDROLASE / CALCIUM TRANSPORT / CALCIUM BINDING / ATP BINDING / ENDOPLASMIC RETICULUM / SARCOPLASMIC RETICULUM / RECOMBINANT
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 / negative regulation of striated muscle contraction / 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 / negative regulation of striated muscle contraction / 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 / intracellular calcium ion homeostasis / calcium ion transport / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / membrane / metal ion binding
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 / 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
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7409
Polymers110,1741
Non-polymers3,5668
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.787, 55.293, 178.278
Angle α, β, γ (deg.)90.00, 118.18, 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 SERCA1a / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1


Mass: 110174.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): COS-7 / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B6CAM1, UniProt: P04191*PLUS

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Non-polymers , 5 types, 15 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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.: 1 / Source method: obtained synthetically / Formula: C16H15N8O13P
#5: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.68 Å3/Da / Density % sol: 66.6 %

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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: 3.2→50 Å / Num. all: 33166 / Num. obs: 32602 / % possible obs: 98.3 % / Observed criterion σ(I): 2.6
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 3.3 % / Rsym value: 0.611 / % possible all: 95.6

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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: 3.2→15 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 74.988 / SU ML: 0.63 / Cross valid method: THROUGHOUT / ESU R Free: 0.542 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29786 1337 5 %RANDOM
Rwork0.26754 ---
obs0.26909 25290 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 153.199 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7689 0 117 7 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.98810781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4955996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.67124.357319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.169151384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0431548
X-RAY DIFFRACTIONr_chiral_restr0.080.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215863
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: 3.2→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 90 -
Rwork0.468 1637 -
obs--95.15 %
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)
10.70250.3942-0.89380.3754-0.18942.08160.05150.3070.16250.1297-0.24060.2141-0.5686-1.28970.18911.7380.0906-0.07031.69440.11470.569552.893-1.547431.9569
21.41270.3267-1.57010.8715-2.47187.54080.1432-0.00660.08440.27980.63970.2117-0.2512-1.7355-0.78291.7408-0.076-0.32640.59090.14550.320873.3793-11.352636.7264
38.256-1.38435.14390.2574-1.047.65880.0008-0.1408-0.09480.03060.10020.05990.6923-0.2277-0.1011.8342-0.0885-0.28090.33940.10860.489488.7117-37.428466.6058
42.9759-1.78581.28993.71350.54253.5803-0.3577-1.2649-0.54080.41260.88360.62630.5667-2.0163-0.52591.5551-0.0952-0.02651.56550.59670.441173.2767-33.609372.1751
54.0751-2.55190.5665.53331.5911.4713-0.19340.054-0.02530.44820.467-0.2647-0.7846-0.01-0.27361.50480.1604-0.26380.4199-0.02880.322393.6662-27.064474.467
64.41930.95122.65950.39020.08063.24240.1573-0.92140.5058-0.03430.07820.2736-0.1509-1.1552-0.23551.87450.371-0.10340.82350.00250.563280.3551-21.348178.6331
71.1219-0.79561.23223.32650.61223.185-0.39340.23890.21610.27150.1959-0.30560.04910.26780.19751.6249-0.0204-0.22150.4577-0.00840.370691.2872-12.17650.742
83.11060.28680.93830.8566-1.62583.9198-0.10470.12450.07560.26930.3650.1203-0.559-0.5091-0.26031.66760.0557-0.17140.51390.13290.344676.5578-7.174147.6357
91.7874-0.41280.82661.7911-1.14595.36450.32380.83270.0549-0.2409-0.25820.12660.5442-0.2235-0.06551.64010.0009-0.14341.07330.1310.171774.3967-4.9840.732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 314
2X-RAY DIFFRACTION2A315 - 358
3X-RAY DIFFRACTION3A359 - 400
4X-RAY DIFFRACTION4A401 - 517
5X-RAY DIFFRACTION5A518 - 557
6X-RAY DIFFRACTION6A558 - 601
7X-RAY DIFFRACTION7A602 - 679
8X-RAY DIFFRACTION8A680 - 747
9X-RAY DIFFRACTION9A748 - 994

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