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- PDB-2g9b: NMR solution structure of CA2+-loaded calbindin D28K -

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Basic information

Entry
Database: PDB / ID: 2g9b
TitleNMR solution structure of CA2+-loaded calbindin D28K
ComponentsCalbindin
KeywordsMETAL BINDING PROTEIN / EF-HAND / CA2+-BINDING
Function / homology
Function and homology information


metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / metanephric part of ureteric bud development / cuticular plate / retina layer formation / response to auditory stimulus / vitamin D metabolic process / short-term memory ...metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / metanephric part of ureteric bud development / cuticular plate / retina layer formation / response to auditory stimulus / vitamin D metabolic process / short-term memory / vitamin D binding / stereocilium / metanephric collecting duct development / cochlea development / postsynaptic cytosol / long-term memory / presynaptic cytosol / calyx of Held / hippocampal mossy fiber to CA3 synapse / GABA-ergic synapse / locomotory behavior / terminal bouton / regulation of synaptic plasticity / retina development in camera-type eye / learning or memory / postsynapse / neuron projection / axon / neuronal cell body / synapse / dendrite / calcium ion binding / glutamatergic synapse / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Calbindin / : / EF hand domain / 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. ...Calbindin / : / EF hand domain / 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
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / Torsion angle dynamics, molecular dynamics simulated annealing refinement in explicit solvent (water)
AuthorsKojetin, D.J. / Venters, R.A. / Kordys, D.R. / Thompson, R.J. / Kumar, R. / Cavanagh, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure, binding interface and hydrophobic transitions of Ca(2+)-loaded calbindin-D(28K).
Authors: Kojetin, D.J. / Venters, R.A. / Kordys, D.R. / Thompson, R.J. / Kumar, R. / Cavanagh, J.
History
DepositionMar 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calbindin


Theoretical massNumber of molelcules
Total (without water)30,1731
Polymers30,1731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 900structures with the least restraint violations, structures with the lowest restraint energy
RepresentativeModel #1fewest violations, lowest restraint energy

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Components

#1: Protein Calbindin / Vitamin D-dependent calcium-binding protein / avian-type / Calbindin D28 / D-28K / Spot 35 protein


Mass: 30173.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Calb1 / Plasmid: PGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P07171

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2114D 13C/15N-separated NOESY
2224D 13C/13C-separated NOESY
1333D CT 13C methyl-separated NOESY
243(4,2)D CT 13C/13C methyl-separated NOESY
1534D 13C/15N-separated NOESY
263(4,2)D 13C/15N-separated NOESY
1744D 15N/15N-separated NOESY
281(4,2)D 13C ali/13C aro-separated NOESY
NMR detailsText: This structure was determined using a combination of 3D, 4D and (4,2)D projection reconstruction techniques on perdeuterated and fully protonated samples.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM calbindin D28k; U-15N,13C; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 90% H2O, 10% D2O90% H2O/10% D2O
21mM calbindin D28k; U-15N,13C; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 100% D2O100% D2O
31mM calbindin D28k; U-2H,15N,13C; Ile (d1 only), Leu, Val methyl protonated; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 90% H2O, 10% D2O90% H2O/10% D2O
41mM calbindin D28k; U-2H,15N; 10 mM Tris, 1 mM DTT, 0.02% NaN3, 6 mM CaCl2, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
16 mM CACL2 7AMBIENT 298 K
26 mM CACL2 6.2AMBIENT 323 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.refinement
NMRPipe2.3Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.structure solution
NMRView5Johnson, B.A., Blevins, R.A.structure solution
XPLOR-NIH2.9.4aSCHWIETERS, C.D. et al.refinement
RefinementMethod: Torsion angle dynamics, molecular dynamics simulated annealing refinement in explicit solvent (water)
Software ordinal: 1
Details: the structures are based on 6882 NOE distance constraints, 432 dihedral angle restraints, 36 hydrogen bond restraints and 304 residual dipolar coupling restraints
NMR representativeSelection criteria: fewest violations, lowest restraint energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest restraint energy
Conformers calculated total number: 900 / Conformers submitted total number: 10

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