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- PDB-3uom: Ca2+ complex of Human skeletal calsequestrin -

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Basic information

Entry
Database: PDB / ID: 3uom
TitleCa2+ complex of Human skeletal calsequestrin
ComponentsCalsequestrin-1
Keywordscalcium-binding protein / Thioredoxin-like fold / Calcium binding / Sarcoplasmic Reticulum
Function / homology
Function and homology information


terminal cisterna lumen / positive regulation of store-operated calcium channel activity / response to denervation involved in regulation of muscle adaptation / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / endoplasmic reticulum organization / sarcomere organization / smooth endoplasmic reticulum / protein polymerization ...terminal cisterna lumen / positive regulation of store-operated calcium channel activity / response to denervation involved in regulation of muscle adaptation / regulation of store-operated calcium entry / sarcoplasmic reticulum lumen / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / endoplasmic reticulum organization / sarcomere organization / smooth endoplasmic reticulum / protein polymerization / skeletal muscle tissue development / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / response to heat / mitochondrial matrix / calcium ion binding / endoplasmic reticulum / mitochondrion / identical protein binding
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: 2.02 Å
AuthorsSanchez, E.J. / Lewis, K.M. / Danna, B.R. / Nissen, M.S. / Kang, C.H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: High-capacity Ca2+ Binding of Human Skeletal Calsequestrin.
Authors: Sanchez, E.J. / Lewis, K.M. / Danna, B.R. / Kang, C.
History
DepositionNov 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_alt_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_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calsequestrin-1
B: Calsequestrin-1
C: Calsequestrin-1
D: Calsequestrin-1
E: Calsequestrin-1
F: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,745134
Polymers250,3356
Non-polymers8,410128
Water21,8701214
1
A: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,11122
Polymers41,7231
Non-polymers1,38821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,15123
Polymers41,7231
Non-polymers1,42822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,15123
Polymers41,7231
Non-polymers1,42822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,15123
Polymers41,7231
Non-polymers1,42822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,95320
Polymers41,7231
Non-polymers1,23019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Calsequestrin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,22923
Polymers41,7231
Non-polymers1,50622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.799, 89.793, 119.161
Angle α, β, γ (deg.)90.13, 89.90, 60.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Calsequestrin-1 / Calmitin / Calsequestrin / skeletal muscle isoform


Mass: 41722.578 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21 / References: UniProt: P31415
#2: Chemical...
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM Bis-tris propane, 50 mM CaCl2, 40% MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.015→50 Å / Num. obs: 195624 / % possible obs: 95.8 %

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1A8Y

1a8y


Resolution: 2.02→38.9 Å / SU ML: 0.22 / σ(F): 0.07 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1906 0.97 %
Rwork0.182 --
obs0.182 195624 91.8 %
all-204132 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.36 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.6043 Å20.4821 Å2-0.4783 Å2
2--2.0518 Å2-0.0848 Å2
3----4.6561 Å2
Refinement stepCycle: LAST / Resolution: 2.02→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17062 0 422 1214 18698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718050
X-RAY DIFFRACTIONf_angle_d1.03324586
X-RAY DIFFRACTIONf_dihedral_angle_d14.9696768
X-RAY DIFFRACTIONf_chiral_restr0.0752651
X-RAY DIFFRACTIONf_plane_restr0.0053235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.015-2.06490.3354900.23659316X-RAY DIFFRACTION62
2.0649-2.12080.21711170.217912364X-RAY DIFFRACTION82
2.1208-2.18320.25641310.202713330X-RAY DIFFRACTION88
2.1832-2.25360.28031500.193913689X-RAY DIFFRACTION91
2.2536-2.33420.18291390.188613825X-RAY DIFFRACTION92
2.3342-2.42760.30461360.187814073X-RAY DIFFRACTION93
2.4276-2.53810.2171400.192514157X-RAY DIFFRACTION94
2.5381-2.67180.23271370.188814320X-RAY DIFFRACTION95
2.6718-2.83920.17571420.186714562X-RAY DIFFRACTION96
2.8392-3.05830.24921500.185814682X-RAY DIFFRACTION97
3.0583-3.36590.2071430.177214737X-RAY DIFFRACTION98
3.3659-3.85260.20111350.162414875X-RAY DIFFRACTION98
3.8526-4.85240.16311380.150314905X-RAY DIFFRACTION99
4.8524-38.91150.21341580.196214883X-RAY DIFFRACTION99

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