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- PDB-5mra: human SCBD (sorcin calcium binding domain) in complex with doxorubicin -

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Basic information

Entry
Database: PDB / ID: 5mra
Titlehuman SCBD (sorcin calcium binding domain) in complex with doxorubicin
ComponentsSorcin
KeywordsMETAL BINDING PROTEIN / Sorcin (soluble resistance-related calcium binding protein)
Function / homology
Function and homology information


regulation of relaxation of muscle / regulation of cell communication by electrical coupling / negative regulation of cardiac muscle contraction / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases ...regulation of relaxation of muscle / regulation of cell communication by electrical coupling / negative regulation of cardiac muscle contraction / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases / regulation of calcium ion transport / transcription regulator inhibitor activity / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T-tubule / sarcoplasmic reticulum membrane / protein sequestering activity / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / calcium channel regulator activity / Stimuli-sensing channels / Z disc / calcium ion transport / protease binding / DNA-binding transcription factor binding / transmembrane transporter binding / protein heterodimerization activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
EF-hand domain / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...EF-hand domain / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DOXORUBICIN / Sorcin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.74 Å
AuthorsIlari, A. / Fiorillo, A. / Colotti, G. / Genovese, I.
CitationJournal: Cell Death Dis / Year: 2017
Title: Binding of doxorubicin to Sorcin impairs cell death and increases drug resistance in cancer cells.
Authors: Genovese, I. / Fiorillo, A. / Ilari, A. / Masciarelli, S. / Fazi, F. / Colotti, G.
History
DepositionDec 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorcin
B: Sorcin
C: Sorcin
D: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,25816
Polymers75,3934
Non-polymers86512
Water181
1
A: Sorcin
B: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4409
Polymers37,6972
Non-polymers7437
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-55 kcal/mol
Surface area15960 Å2
MethodPISA
2
C: Sorcin
D: Sorcin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8187
Polymers37,6972
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-61 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.229, 104.831, 113.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Sorcin / 22 kDa protein / CP-22 / CP22 / V19


Mass: 18848.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRI / Production host: Escherichia coli (E. coli) / References: UniProt: P30626
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11 / Comment: medication, chemotherapy*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M MgCl2, 0.1 M Tris pH=7, NaCl 2.5 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.74→76.94 Å / Num. obs: 11800 / % possible obs: 99 % / Redundancy: 6.53 % / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.81
Reflection shellResolution: 3.74→3.96 Å / Redundancy: 6.47 % / Mean I/σ(I) obs: 1.45 / CC1/2: 0.561 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UPG

4upg


Resolution: 3.74→76.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28501 569 4.8 %RANDOM
Rwork0.19185 ---
obs0.19623 11193 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 177.223 Å2
Baniso -1Baniso -2Baniso -3
1--7.39 Å2-0 Å2-0 Å2
2---1.22 Å20 Å2
3---8.61 Å2
Refinement stepCycle: 1 / Resolution: 3.74→76.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 53 1 5280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.025376
X-RAY DIFFRACTIONr_bond_other_d0.0020.024910
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9547277
X-RAY DIFFRACTIONr_angle_other_deg1.001311241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9885664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36223.955268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.69915872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0641541
X-RAY DIFFRACTIONr_chiral_restr0.0670.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021327
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_it9.83717.7752668
X-RAY DIFFRACTIONr_mcbond_other9.83417.7742667
X-RAY DIFFRACTIONr_mcangle_it15.74626.6283328
X-RAY DIFFRACTIONr_mcangle_other15.74326.6293329
X-RAY DIFFRACTIONr_scbond_it8.50118.2492708
X-RAY DIFFRACTIONr_scbond_other8.518.2522709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.18427.2073950
X-RAY DIFFRACTIONr_long_range_B_refined21.046492
X-RAY DIFFRACTIONr_long_range_B_other21.0386493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.74→3.833 Å
RfactorNum. reflection% reflection
Rfree0.37 46 -
Rwork0.35 765 -
obs--94.52 %

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