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- PDB-1mwn: Solution NMR structure of S100B bound to the high-affinity target... -

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Basic information

Entry
Database: PDB / ID: 1mwn
TitleSolution NMR structure of S100B bound to the high-affinity target peptide TRTK-12
Components
  • F-actin capping protein alpha-1 subunit
  • S-100 protein, beta chain
KeywordsSTRUCTURAL PROTEIN / S100B / TRTK-12 / Calcium-binding / EF-hand / S100 protein / four helix bundle / helix loop helix / protein-peptide complex / 20 structures
Function / homology
Function and homology information


TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of skeletal muscle cell differentiation / F-actin capping protein complex / WASH complex / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination ...TAK1-dependent IKK and NF-kappa-B activation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of skeletal muscle cell differentiation / F-actin capping protein complex / WASH complex / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / positive regulation of myelination / cell junction assembly / barbed-end actin filament capping / response to methylmercury / astrocyte differentiation / S100 protein binding / COPI-independent Golgi-to-ER retrograde traffic / neuron projection extension / Sensory processing of sound by inner hair cells of the cochlea / response to anesthetic / cortical cytoskeleton / Advanced glycosylation endproduct receptor signaling / regulation of neuronal synaptic plasticity / positive regulation of synaptic transmission / COPI-mediated anterograde transport / ruffle / positive regulation of neuron differentiation / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to glucocorticoid / tau protein binding / memory / long-term synaptic potentiation / calcium-dependent protein binding / actin filament binding / regulation of cell shape / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / actin binding / actin cytoskeleton organization / protein-containing complex assembly / response to ethanol / cellular response to hypoxia / learning or memory / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / cell adhesion / ciliary basal body / positive regulation of apoptotic process / cadherin binding / signaling receptor binding / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein S100-B / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / S-100/ICaBP type calcium binding protein signature. ...Protein S100-B / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / 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
Protein S100-B / F-actin-capping protein subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsInman, K.G. / Yang, R. / Rustandi, R.R. / Miller, K.E. / Baldisseri, D.M. / Weber, D.J.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12
Authors: Inman, K.G. / Yang, R. / Rustandi, R.R. / Miller, K.E. / Baldisseri, D.M. / Weber, D.J.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the negative regulatory domain of p53 bound to S100B(betabeta)
Authors: Rustandi, R.R. / Baldisseri, D.M. / Weber, D.J.
#2: Journal: Biochemistry / Year: 1998
Title: Solution structure of calcium-bound rat S100B(betabeta) as determined by nuclear magnetic resonance spectroscopy
Authors: Drohat, A.C. / Baldisseri, D.M. / Rustandi, R.R. / Weber, D.J.
#3: Journal: Biochemistry / Year: 1996
Title: Solution structure of rat apo-S100B(betabeta) as determined by NMR spectroscopy
Authors: Drohat, A.C. / Amburgey, J.C. / Abildgaard, F. / Starich, M.R. / Baldisseri, D.M. / Weber, D.J.
History
DepositionSep 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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
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
X: F-actin capping protein alpha-1 subunit
Y: F-actin capping protein alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6328
Polymers24,4724
Non-polymers1604
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 / 200structures with the lowest energy
RepresentativeModel #2closest to the average

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Components

#1: Protein S-100 protein, beta chain / S100B


Mass: 10758.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: S100B / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 (DE3) / References: UniProt: P04631
#2: Protein/peptide F-actin capping protein alpha-1 subunit / CapZ alpha-1 / CAPZA1 / TRTK-12


Mass: 1477.728 Da / Num. of mol.: 2 / Fragment: Residues 265-276 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P52907
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C-separated NOESY
1214D 13C/15N-separated NOESY
1313D 15N-separated NOESY
1412D NOESY
1513D 13C-filter NOESY
1612D TOCSY
171HNHA
NMR detailsText: This structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2.2 mM S100B (subunit concentration), 5.2 mM CaCl2, 2.6 mM TRTK-12 peptide, 10 mM tris-d11, 15 mM NaCl, 0.1 mM EDTA, 5 mM DTT, 0.35 mM NaN3
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 25 mM / pH: 6.5 / Pressure: ambient / Temperature: 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 DMXBrukerDMX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
NMRPipeDelagliodata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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