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- PDB-1psb: Solution structure of calcium loaded S100B complexed to a peptide... -

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Basic information

Entry
Database: PDB / ID: 1psb
TitleSolution structure of calcium loaded S100B complexed to a peptide from N-Terminal regulatory domain of NDR kinase.
Components
  • Ndr Ser/Thr kinase-like protein
  • S-100 protein, beta chain
KeywordsMETAL BINDING PROTEIN / HELIX-LOOP-HELIX / PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / postsynapse organization / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production ...Advanced glycosylation endproduct receptor signaling / TRAF6 mediated NF-kB activation / TAK1-dependent IKK and NF-kappa-B activation / postsynapse organization / adaptive thermogenesis / kinase inhibitor activity / sympathetic neuron projection extension / positive regulation of complement activation / RAGE receptor binding / negative regulation of monocyte chemotactic protein-1 production / mitogen-activated protein kinase kinase kinase binding / S100 protein binding / RHOBTB1 GTPase cycle / RHOBTB2 GTPase cycle / axonogenesis / negative regulation of MAP kinase activity / sarcoplasmic reticulum / astrocyte activation / protein modification process / tau protein binding / calcium-dependent protein binding / regulation of translation / positive regulation of canonical NF-kappaB signal transduction / learning or memory / non-specific serine/threonine protein kinase / cell adhesion / intracellular signal transduction / cadherin binding / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Protein kinase, C-terminal / Protein kinase C terminal domain / EF hand / Extension to Ser/Thr-type protein kinases ...Protein S100-B / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Protein kinase, C-terminal / Protein kinase C terminal domain / EF hand / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / EF-hand / Recoverin; domain 1 / 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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein S100-B / Serine/threonine-protein kinase 38
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / Torsion Angle Dynamics, Restrained Molecular Dynamics, Simulated Annealing,
AuthorsBhattacharya, S. / Large, E. / Heizmann, C.W. / Hemmings, B. / Chazin, W.J.
CitationJournal: Biochemistry / Year: 2003
Title: Structure of the Ca(2+)/S100B/NDR Kinase Peptide Complex: Insights into S100 Target Specificity and Activation of the Kinase.
Authors: Bhattacharya, S. / Large, E. / Heizmann, C.W. / Hemmings, B. / Chazin, W.J.
History
DepositionJun 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 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: S-100 protein, beta chain
B: S-100 protein, beta chain
C: Ndr Ser/Thr kinase-like protein
D: Ndr Ser/Thr kinase-like protein


Theoretical massNumber of molelcules
Total (without water)27,5674
Polymers27,5674
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)20 / 128structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein S-100 protein, beta chain


Mass: 10550.776 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: S100B / Plasmid: pH6 TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3) RIL / References: UniProt: P02638
#2: Protein/peptide Ndr Ser/Thr kinase-like protein


Mass: 3232.855 Da / Num. of mol.: 2
Fragment: N-terminal regulatory domain fragment, sequence database residue 60-85
Source method: obtained synthetically / Details: This sequence occurs naturally in Homo sapiens. / References: UniProt: Q15208

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
3333D 13C-separated NOESY
2422D 15N/13C F2-Filtered NOESY
2523D 13C-F1 separated 13C/15N-F2 Filtered HMQC-NOESY
NMR detailsText: Protein Backbone/Side-Chain Assignments were made from 3D CBCA(CO)NH, 3D HNCA, 3D HN(CO)CA, 3D HNCO 3D HCCH-TOCSY, 3D HCCH-COSY experiments. Peptide was assigned from 2D-Filtered COSY/TOCSY Experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 1H,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL90% H2O/10% D2O
21 mM 1H,13C,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL90% H2O/10% D2O
31 mM 1H,13C,15N labeled protein 1 mM unlabeled peptide 20 mM d-11 tris and 10mM d10-DTT 5 mM CaCl2 and 30mM KCL100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.045 M/L 7.5 ambient 310 K
20.045 M/L 7.5 ambient 310 K
30.045 M/L 7.5 ambient 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
Felix2000Accelrysprocessing
Felix2000Accelrysdata analysis
DYANA1.5Guentertstructure solution
Amber7Pearlman, Case, Caldwell, Seibel, Chandra Singh, Weiner, Kollmanrefinement
RefinementMethod: Torsion Angle Dynamics, Restrained Molecular Dynamics, Simulated Annealing,
Software ordinal: 1
Details: The structures are based on a total of 3274 restraints, 2964 are NOE-derived distance constraints and 310 dihedral angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 128 / Conformers submitted total number: 20

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