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- PDB-6owv: Crystal structure of a Human Cardiac Calsequestrin Filament -

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Basic information

Entry
Database: PDB / ID: 6owv
TitleCrystal structure of a Human Cardiac Calsequestrin Filament
ComponentsCalsequestrin-2
KeywordsMETAL BINDING PROTEIN / Calsequestrin / Calcium-Binding Proteins / Sarcoplasmic Reticulum Proteins
Function / homology
Function and homology information


calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / sequestering of calcium ion / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / cellular response to caffeine / negative regulation of ryanodine-sensitive calcium-release channel activity ...calcium ion sequestering activity / negative regulation of potassium ion transmembrane transporter activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / sequestering of calcium ion / Purkinje myocyte to ventricular cardiac muscle cell signaling / sarcoplasmic reticulum lumen / regulation of membrane repolarization / cellular response to caffeine / negative regulation of ryanodine-sensitive calcium-release channel activity / negative regulation of potassium ion transport / detection of calcium ion / protein polymerization / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cardiac muscle contraction / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / calcium channel complex / sarcoplasmic reticulum membrane / regulation of heart rate / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / intracellular calcium ion homeostasis / calcium-dependent protein binding / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin ...Calsequestrin / Calsequestrin, conserved site / Calsequestrin, middle TRX-fold domain / Calsequestrin, N-terminal TRX-fold domain / Calsequestrin, C-terminal TRX-fold domain / Calsequestrin / Calsequestrin signature 1. / Calsequestrin signature 2. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsTitus, E.W. / Deiter, F.H. / Shi, C. / Jura, N. / Deo, R.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)F30HL137329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007618 United States
American Heart Association17IRG33460152 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)DP2HL123228 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: The structure of a calsequestrin filament reveals mechanisms of familial arrhythmia.
Authors: Titus, E.W. / Deiter, F.H. / Shi, C. / Wojciak, J. / Scheinman, M. / Jura, N. / Deo, R.C.
History
DepositionMay 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Dec 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 1.4Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,04728
Polymers44,9691
Non-polymers1,07827
Water59433
1
A: Calsequestrin-2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)276,283168
Polymers269,8126
Non-polymers6,471162
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-y+1,x,z-1/41
crystal symmetry operation4_565y,-x+1,z+1/41
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation7_555y,x,-z+1/41
crystal symmetry operation8_664-y+1,-x+1,-z-1/41
Unit cell
Length a, b, c (Å)62.533, 62.533, 213.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21A-402-

SO4

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Components

#1: Protein Calsequestrin-2 / Calsequestrin / cardiac muscle isoform


Mass: 44968.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASQ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O14958
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.89 % / Description: Rod
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, lithium sulfate / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.88→71.06 Å / Num. obs: 35602 / % possible obs: 100 % / Redundancy: 22.5 % / Biso Wilson estimate: 47.702 Å2 / Rpim(I) all: 0.018 / Rrim(I) all: 0.086 / Net I/σ(I): 14.8 / Num. measured all: 799805
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.88-1.9111.70.42003517113.23411.05298.6
5.1-71.1121.747.34411420350.0110.048100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Blu-Icedata collection
ELVESdata processing
DIALSdata reduction
DIALSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SJI

1sji


Resolution: 1.88→53.937 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1767 5.08 %
Rwork0.213 32993 -
obs0.2149 34760 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.99 Å2 / Biso mean: 82.651 Å2 / Biso min: 38.92 Å2
Refinement stepCycle: final / Resolution: 1.88→53.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 35 33 2783
Biso mean--120.14 55.83 -
Num. residues----329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.93060.5139890.5062189075
1.9306-1.98740.39051260.3656247398
1.9874-2.05150.30451330.3175255199
2.0515-2.12490.32191180.2855255199
2.1249-2.20990.32631460.2762532100
2.2099-2.31050.35741330.30412557100
2.3105-2.43230.34781440.26872536100
2.4323-2.58470.2991380.2492588100
2.5847-2.78430.2771380.25352585100
2.7843-3.06440.27891380.24932596100
3.0644-3.50780.2531520.22322627100
3.5078-4.41920.2041490.18192660100
4.4192-53.9370.22251630.1752847100
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)
13.5731-0.24750.22548.42531.20667.1221-0.08280.4226-0.88310.18240.30390.73711.8594-0.6593-0.17420.9786-0.097-0.05080.6162-0.01040.644121.58742.0912.5719
23.2272-0.1148-0.24163.02630.66147.83380.14950.5010.0304-0.2753-0.09310.2041-0.1951-0.9376-0.02410.30680.0971-0.00980.56350.02540.393315.591730.421513.2694
34.19630.34470.3857.1798-0.65426.10090.0137-0.1802-0.1288-0.01190.06550.57680.0535-1.17020.00490.2732-0.0723-0.00130.71540.06090.42418.953525.2408-14.0346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 141 )A23 - 141
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 268 )A142 - 268
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 371 )A269 - 371

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