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- PDB-3j7t: Calcium atpase structure with two bound calcium ions determined b... -

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Basic information

Entry
Database: PDB / ID: 3j7t
TitleCalcium atpase structure with two bound calcium ions determined by electron crystallography of thin 3D crystals
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / ION PUMP / MEMBRANE PROTEIN / P-TYPE ATPASE / ACTIVE 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
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3.4 Å
AuthorsYonekura, K. / Kato, K. / Ogasawara, M. / Tomita, M. / Toyoshima, C.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.
Authors: Koji Yonekura / Kazuyuki Kato / Mitsuo Ogasawara / Masahiro Tomita / Chikashi Toyoshima /
Abstract: Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for ...Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.
History
DepositionAug 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,7064
Polymers109,6031
Non-polymers1033
Water2,792155
1
A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules

A: Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,4118
Polymers219,2052
Non-polymers2066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2360 Å2
ΔGint-71 kcal/mol
Surface area91440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.300, 64.402, 147.316
Angle α, β, γ (deg.)90.00, 98.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 / SERCA1 / SR Ca(2+)-ATPase 1 / Calcium pump 1 / Calcium-transporting ATPase sarcoplasmic reticulum ...SERCA1 / 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: 109602.578 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 994 G IN THIS STRUCTURE IS NATURAL VARIATION ACCORDING TO DATABASE P04191-2 (AT2A1_RABIT) ...RESIDUE 994 G IN THIS STRUCTURE IS NATURAL VARIATION ACCORDING TO DATABASE P04191-2 (AT2A1_RABIT) ISOFORM SERCA1A. C-TERMINAL RESIDUES 994-1001 (DPEDERRK) ARE REPLACED BY G IN ISOFORM SERCA1A.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: calcium ATPase / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

MicroscopyModel: HITACHI HF3000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingFilm or detector model: TVIPS TEMCAM-F224 (2k x 2k)

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
3D reconstructionSymmetry type: 3D CRYSTAL
RefinementResolution: 3.4→8 Å / Cor.coef. Fo:Fc: 0.798 / Cor.coef. Fo:Fc free: 0.768 / SU B: 27.539 / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.939 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3152 436 3 %RANDOM
Rwork0.2769 14184 --
obs0.278 -67.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 98.19 Å2 / Biso mean: 29.835 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--4.96 Å2-0 Å21.21 Å2
2---5.94 Å2-0 Å2
3---10.28 Å2
Refinement stepCycle: LAST / Resolution: 3.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7670 0 3 155 7828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0060.0198206
ELECTRON CRYSTALLOGRAPHYr_bond_other_d0.0010.027691
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.0292.03211250
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.769317193
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg5.6535993
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg36.53924.357319
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg17.001151382
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_4_deg15.8071548
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0560.21235
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0040.0218955
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0010.021441
LS refinement shellResolution: 3.4→3.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 27 -
Rwork0.356 678 -
all-705 -
obs--65.7 %

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