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- PDB-2jc2: The crystal structure of the natural F112L human sorcin mutant -

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Basic information

Entry
Database: PDB / ID: 2jc2
TitleThe crystal structure of the natural F112L human sorcin mutant
ComponentsSORCIN
KeywordsMETAL BINDING PROTEIN / RYANODINE RECEPTOR INTERACTING PROTEIN / CALCIUM BINDING PROTEIN / NATURAL F112L SORCIN MUTANT / CALCIUM
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 / regulation of calcium ion transport ...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 / regulation of calcium ion transport / Ion transport by P-type ATPases / transcription regulator inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / protein sequestering activity / sarcoplasmic reticulum / positive regulation of release of sequestered calcium ion into cytosol / 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 / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #900 / EF-hand domain / EF-hand domain pair / Helix Hairpins / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair / Special / EF-hand, calcium binding motif ...Helix Hairpins - #900 / EF-hand domain / EF-hand domain pair / Helix Hairpins / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair / Special / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFranceschini, S. / Ilari, A. / Colotti, G. / Chiancone, E.
Citation
Journal: Faseb J. / Year: 2008
Title: Molecular Basis for the Impaired Function of the Natural F112L Sorcin Mutant: X-Ray Crystal Structure, Calcium Affinity, and Interaction with Annexin Vii and the Ryanodine Receptor.
Authors: Franceschini, S. / Ilari, A. / Verzili, D. / Zamparelli, C. / Antaramian, A. / Rueda, A. / Valdivia, H.H. / Chiancone, E. / Colotti, G.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: The Crystal Structure of the Sorcin Calcium Binding Domain Provides a Model of Calcium-Dependent Processes in the Full Length Protein
Authors: Ilari, A. / Johnson, K.A. / Nastopoulos, V. / Verzili, D. / Zamparelli, C. / Colotti, G. / Tsernoglou, D. / Chiancone, E.
#2: Journal: Protein Sci. / Year: 2001
Title: Crystal Structure of Calcium-Free Human Sorcin: A Member of the Penta-EF-Hand Protein Family
Authors: Xie, X. / Dwyer, M.D. / Swenson, L. / Parker, M.H. / Botfield, M.C.
History
DepositionDec 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)87,22210
Polymers86,6454
Non-polymers5766
Water2,522140
1
A: SORCIN
B: SORCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6115
Polymers43,3232
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-21.2 kcal/mol
Surface area24200 Å2
MethodPQS
2
C: SORCIN
D: SORCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6115
Polymers43,3232
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-20.3 kcal/mol
Surface area24100 Å2
MethodPQS
Unit cell
Length a, b, c (Å)64.385, 64.385, 314.837
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 33 - 198 / Label seq-ID: 33 - 198

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.50028, 0.86586, -0.00026), (0.86586, -0.50028, -0.00031), (-0.0004, -7.0E-5, -1)
Vector: -0.00514, 0.01559, -0.02023)

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Components

#1: Protein
SORCIN / 22 KDA PROTEIN / CP-22 / V19 / F112L HUMAN SORCIN MUTANT


Mass: 21661.320 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: HEART, MUSCLE, BRAIN AND ADRENAL MEDULLA / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30626
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 112 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 112 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, PHE 112 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 112 TO LEU ENGINEERED RESIDUE IN CHAIN C, PHE 112 TO LEU ENGINEERED RESIDUE IN CHAIN D, PHE 112 TO LEU
Sequence detailsF112L IS A NATURAL HUMAN SORCIN MUTANT.

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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: 2.51 Å3/Da / Density % sol: 50.52 % / Description: NONE
Crystal growpH: 5.7 / Details: AMMONIUM SULFATE 1.0M, PH 5.7, 12% V/V DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 25105 / % possible obs: 96.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 85.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JUO

1juo


Resolution: 2.5→45.5 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.596 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 1.059 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM M1 TO Q32 ARE MISSING IN THE STRUCTURE BECAUSE OF AN INSUFFICIENT ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1230 5 %RANDOM
Rwork0.252 ---
obs0.254 23442 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 30 140 5352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225306
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8511.957179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0415660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66623.87261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.041542
X-RAY DIFFRACTIONr_chiral_restr0.0530.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024078
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1670.22454
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.23753
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.261.53397
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46625265
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.52932200
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8424.51914
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 1292 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional00.05
1Atight thermal0.010.5
2Btight thermal0.010.5
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 85
Rwork0.307 1512

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