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- PDB-2pru: NMR Structure of Human apoS100B at 10C -

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Basic information

Entry
Database: PDB / ID: 2pru
TitleNMR Structure of Human apoS100B at 10C
ComponentsProtein S100-B
KeywordsMETAL BINDING PROTEIN / S100 / Calcium Binding Protein / EF-hand / all alpha helical protein
Function / homology
Function and homology information


negative regulation of skeletal muscle cell differentiation / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination / response to methylmercury / astrocyte differentiation / S100 protein binding / response to anesthetic / TRAF6 mediated NF-kB activation ...negative regulation of skeletal muscle cell differentiation / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination / response to methylmercury / astrocyte differentiation / S100 protein binding / response to anesthetic / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / regulation of neuronal synaptic plasticity / Nuclear signaling by ERBB4 / ruffle / positive regulation of neuron differentiation / axonogenesis / response to glucocorticoid / central nervous system development / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / long-term synaptic potentiation / calcium-dependent protein binding / regulation of cell shape / microtubule cytoskeleton / cellular response to hypoxia / learning or memory / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / cilium / ciliary basal body / positive regulation of apoptotic process / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...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 / EF hand domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / CNS - non-crystallograqphic symmetry for the homodimer, distance geometry, simulated annealing, molecular dynamics. Final Refinement in the presence of explicit solvent.
AuthorsMalik, S. / Shaw, G.S. / Revington, M.
CitationJournal: Proteins / Year: 2008
Title: Analysis of the structure of human apo-S100B at low temperature indicates a unimodal conformational distribution is adopted by calcium-free S100 proteins.
Authors: Malik, S. / Revington, M. / Smith, S.P. / Shaw, G.S.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 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: Protein S100-B
B: Protein S100-B


Theoretical massNumber of molelcules
Total (without water)21,1922
Polymers21,1922
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 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein S100-B / S100 calcium-binding protein B / S-100 protein beta subunit / S-100 protein beta chain


Mass: 10595.841 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100B / Plasmid: pSS2 from pSD80 / Production host: Escherichia coli (E. coli) / Strain (production host): N99 / References: UniProt: P04271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
13215N IPAP-HSQC for Residual dipolar couplings
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM U-13C,U-15N S100B, 50 mM KCl, 90%H2O/10%D2O90% H2O/10% D2O
20.7 mM U-15N S100B, 50 mM KCl, 12 mg/ml PF1 Phage, 90%H2O/10%D2O90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 7.2 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
VNMR6.1BVarian Associatescollection
NMRView5.2.2B.A. Johnson and R.A. Blevinsdata analysis
CNS1.1Brunger AT,Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW,Jiang JS,Kuszewski J, Nilges M, Pannu NS, Read, RJ, Rice, LM, Simonson T, and Warren, GLrefinement
RECOORD1Nederveen AJ, Doreleijers JF, Vranken W, Miller Z, Spronk CAEM, Nabuurs SB, G ntert P, Livny M, Markley JL, Nilges M, Ulrich EL, Kaptein R, Bonvin AMJJrefinement
RefinementMethod: CNS - non-crystallograqphic symmetry for the homodimer, distance geometry, simulated annealing, molecular dynamics. Final Refinement in the presence of explicit solvent.
Software ordinal: 1 / Details: 2504 NOEs, 124 Hbond distance restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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