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- PDB-6rb2: Structure of the (SR)Ca2+-ATPase mutant E340A in the Ca2-E1-CaAMP... -

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Basic information

Entry
Database: PDB / ID: 6rb2
TitleStructure of the (SR)Ca2+-ATPase mutant E340A in the Ca2-E1-CaAMPPCP form
ComponentsSarcoplasmic/endoplasmic reticulum calcium ATPase 1
KeywordsHYDROLASE / Mutant E340A / P-type ATPase / Calcium-transporting ATPase / sarcoplasmic reticulum
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
Similarity search - Function
P-type ATPase, subfamily IIA, SERCA-type / 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, subfamily IIA, SERCA-type / 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 superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / : / Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.20001129942 Å
AuthorsClausen, J.D. / Montigny, C. / Lenoir, G. / Arnou, B. / Jaxel, C. / Moller, J.V. / Nissen, P. / Andersen, J.P. / Le Maire, M. / Bublitz, M.
Funding support France, 1items
OrganizationGrant numberCountry
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05 France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The SERCA residue Glu340 mediates interdomain communication that guides Ca 2+ transport.
Authors: Geurts, M.M.G. / Clausen, J.D. / Arnou, B. / Montigny, C. / Lenoir, G. / Corey, R.A. / Jaxel, C. / Moller, J.V. / Nissen, P. / Andersen, J.P. / le Maire, M. / Bublitz, M.
History
DepositionApr 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,2096
Polymers109,5451
Non-polymers6655
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-26 kcal/mol
Surface area44410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.8999939, 126.9899979, 49.81000137
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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: 109544.539 Da / Num. of mol.: 1 / Mutation: E340A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ATP2A1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04191, P-type Ca2+ transporter
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.36 Å3/Da / Density % sol: 63.42 % / Description: long, square sticks
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG 6000, 10 mM CaCl2, 3 mM MgCl2, 1 mM AMPPCP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 3.2→75 Å / Num. obs: 25331 / % possible obs: 99.9 % / Redundancy: 6.08 % / Biso Wilson estimate: 79.7683784393 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.197 / Net I/σ(I): 10.92
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 2201 / CC1/2: 0.47 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1685refinement
Cootmodel building
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5S

1t5s


Resolution: 3.20001129942→49.81000137 Å / SU ML: 0.481743239297 / Cross valid method: FREE R-VALUE / σ(F): 1.35194034342 / Phase error: 27.2511685647
RfactorNum. reflection% reflectionSelection details
Rfree0.256557153783 1274 5.02941060361 %Random selection
Rwork0.211852798195 24057 --
obs0.214187415331 25331 99.9289912817 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.672110755 Å2
Refinement stepCycle: LAST / Resolution: 3.20001129942→49.81000137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7667 0 35 4 7706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006675193469267865
X-RAY DIFFRACTIONf_angle_d0.70241487476710641
X-RAY DIFFRACTIONf_chiral_restr0.02571942970531235
X-RAY DIFFRACTIONf_plane_restr0.003897302248971358
X-RAY DIFFRACTIONf_dihedral_angle_d12.42476835612930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.32810.380822427951480.3337325553162652X-RAY DIFFRACTION99.8929718159
3.3281-3.47950.339070089241350.2859402278882577X-RAY DIFFRACTION100
3.4795-3.66290.3053619580411380.2512550387592623X-RAY DIFFRACTION99.9637943519
3.6629-3.89230.2962705352371390.2414931814482642X-RAY DIFFRACTION99.928135106
3.8923-4.19270.2608527017491400.1988012774062647X-RAY DIFFRACTION100
4.1927-4.61440.2258290067471400.167663752482662X-RAY DIFFRACTION99.9643239386
4.6144-5.28150.2302309683171410.1772289826332672X-RAY DIFFRACTION99.9644633973
5.2815-6.65160.2404362096321430.2210771992842718X-RAY DIFFRACTION100
6.6516-49.8160.2166023888491500.1907113641672864X-RAY DIFFRACTION99.6693121693

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