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- PDB-1mq1: Ca2+-S100B-TRTK-12 complex -

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Basic information

Entry
Database: PDB / ID: 1mq1
TitleCa2+-S100B-TRTK-12 complex
Components
  • F-actin capping protein alpha-1 subunit
  • S-100 protein, beta chain
KeywordsMETAL BINDING PROTEIN / protein-peptide complex / EF-hand
Function / homology
Function and homology information


F-actin capping protein complex / WASH complex / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / cell junction assembly / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / S100 protein binding / Sensory processing of sound by inner hair cells of the cochlea ...F-actin capping protein complex / WASH complex / adaptive thermogenesis / sympathetic neuron projection extension / RAGE receptor binding / cell junction assembly / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / S100 protein binding / Sensory processing of sound by inner hair cells of the cochlea / cortical cytoskeleton / regulation of neuronal synaptic plasticity / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / COPI-mediated anterograde transport / Nuclear signaling by ERBB4 / ruffle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / positive regulation of neuron differentiation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / central nervous system development / TAK1-dependent IKK and NF-kappa-B activation / tau protein binding / memory / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / actin binding / actin cytoskeleton organization / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / learning or memory / cytoskeleton / cell adhesion / cadherin binding / intracellular membrane-bounded organelle / neuronal cell body / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsMcClintock, K.A. / Shaw, G.S.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A novel S100 target conformation is revealed by the solution structure of the Ca2+-S100B-TRTK-12 complex.
Authors: McClintock, K.A. / Shaw, G.S.
History
DepositionSep 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: F-actin capping protein alpha-1 subunit
D: F-actin capping protein alpha-1 subunit


Theoretical massNumber of molelcules
Total (without water)24,1474
Polymers24,1474
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)17 / 80structures with the lowest energy
RepresentativeModel #16closest to the average

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Components

#1: Protein 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: S100beta / Plasmid: pSS2 / Production host: Escherichia coli (E. coli) / Strain (production host): N99 / References: UniProt: P04271
#2: Protein/peptide F-actin capping protein alpha-1 subunit / CapZ alpha-1 / TRTK-12 peptide


Mass: 1477.728 Da / Num. of mol.: 2 / Fragment: TRTK-12 peptide, RESIDUES 265-276 / Source method: obtained synthetically / Details: The peptide is chemically synthesized. / References: UniProt: P52907

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1333D 13C/15N-separated NOESY
1413D 13C/15N-separated NOESY
1513D 15N-separated NOESY
16413C f1-edited,f3-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-13C, U-15N S100B (1.0 mM) unlabelled TRTK-12 (1.2 mM) 3 mM CaCl290% H20, 10% D20
2U-2H, U-15N S100B (0.35 mM) unlabelled TRTK-12 (0.80 mM) 1 mM CaCl290% H20, 10% D20
3U-13C, U-15N S100B (1.0 mM) 13C-acetyl, 13C-Ile TRTK-12 (1.2 mM) 3 mM CaCl290% H20, 10% D20
4U-13C/U-12C S100B heterodimer (1.0mM) Unlabelled TRTK-12 (1.2 mM) 3 mM CaCl290% H20, 10% D20
Sample conditionsIonic strength: 35 mM KCl / pH: 7.05 / Pressure: ambient / Temperature: 308 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
Varian UNITYVarianUNITY5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1B/ 6.1CVarian, Inc.collection
NMRPipe2.1Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.processing
PIPP4.3.3Garrett, D.S., Powers, R., Gronenborn, A.M., Clore, G.M.data analysis
CNS1.1Brunger, A., Adams, P.D., Clore, G.M., Delano, W.I., 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.I.structure solution
CNS1.1Brunger et.al.refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 17

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