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- PDB-6oww: Crystal structure of a Human Cardiac Calsequestrin Filament Compl... -

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Basic information

Entry
Database: PDB / ID: 6oww
TitleCrystal structure of a Human Cardiac Calsequestrin Filament Complexed with Ytterbium
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 / ion binding / cellular response to caffeine ...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 / ion binding / cellular response to caffeine / negative regulation of potassium ion transport / detection of calcium ion / protein polymerization / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / 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
YTTERBIUM (III) ION / Calsequestrin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 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 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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
B: Calsequestrin-2
C: Calsequestrin-2
D: Calsequestrin-2
E: Calsequestrin-2
F: Calsequestrin-2
G: Calsequestrin-2
H: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)371,13176
Polymers359,7498
Non-polymers11,38268
Water00
1
A: Calsequestrin-2
hetero molecules

F: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89820
Polymers89,9372
Non-polymers2,96118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
2
B: Calsequestrin-2
E: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,80219
Polymers89,9372
Non-polymers2,86517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calsequestrin-2
H: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,62918
Polymers89,9372
Non-polymers2,69216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calsequestrin-2
G: Calsequestrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,80219
Polymers89,9372
Non-polymers2,86517
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.832, 86.015, 214.340
Angle α, β, γ (deg.)90.000, 89.910, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 44968.637 Da / Num. of mol.: 8
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-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 63 / Source method: obtained synthetically / Formula: Yb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.19 %
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: 1.3857 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3857 Å / Relative weight: 1
ReflectionResolution: 3.84→214.34 Å / Num. obs: 29912 / % possible obs: 98.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 59.129 Å2 / Rpim(I) all: 0.162 / Rrim(I) all: 0.548 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3.84-3.9111.60.81733214990.993.40297.8
10.42-214.6710.519.21661615750.0380.12699.1

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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: 6OWV

6owv


Resolution: 3.84→214.34 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 37.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3401 2799 4.86 %
Rwork0.2898 54798 -
obs0.2922 29777 98.39 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 347.97 Å2 / Biso mean: 98.7266 Å2 / Biso min: 41.16 Å2
Refinement stepCycle: final / Resolution: 3.84→214.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21720 0 88 0 21808
Biso mean--141.39 --
Num. residues----2632
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.84-3.90580.42461200.3644278997
3.9058-3.97690.42011700.3559259497
3.9769-4.05340.50711500.3619280798
4.0534-4.13610.42881140.3457266998
4.1361-4.22610.3321200.3223279098
4.2261-4.32440.42931500.2968277799
4.3244-4.43250.3182840.2862275198
4.4325-4.55240.388820.2915283498
4.5524-4.68630.3531210.2957271899
4.6863-4.83760.32981820.305270899
4.8376-5.01050.30931240.2768275298
5.0105-5.21120.34921240.2977271698
5.2112-5.44830.33931580.2891273798
5.4483-5.73560.37321600.2983277698
5.7356-6.0950.37261560.2999272499
6.095-6.56560.33871120.2848274999
6.5656-7.22640.32772150.2885271299
7.2264-8.27210.32061370.2558275499
8.2721-10.4220.28711650.1954273399
10.422-214.340.24951550.2722270898

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