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- PDB-2jtt: Solution structure of calcium loaded S100A6 bound to C-terminal S... -

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Basic information

Entry
Database: PDB / ID: 2jtt
TitleSolution structure of calcium loaded S100A6 bound to C-terminal Siah-1 interacting protein
Components
  • Calcyclin-binding protein
  • Protein S100-A6
Keywordscalcium binding protein/antitumor protein / S100A6 / Siah-1 interacting protein / ubiquitination / E3 ligase complex / beta-catenin / Calcium / Cell cycle / Mitogen / Cytoplasm / Nucleus / Phosphorylation / Ubl conjugation pathway / calcium binding protein-antitumor protein COMPLEX
Function / homology
Function and homology information


cardiac muscle cell differentiation / beta-catenin destruction complex / response to growth hormone / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / tubulin binding / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / cytoplasmic side of plasma membrane ...cardiac muscle cell differentiation / beta-catenin destruction complex / response to growth hormone / S100 protein binding / SCF ubiquitin ligase complex / nuclear envelope lumen / tubulin binding / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / cytoplasmic side of plasma membrane / calcium-dependent protein binding / nuclear envelope / heart development / cell body / collagen-containing extracellular matrix / molecular adaptor activity / protein domain specific binding / ubiquitin protein ligase binding / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / Siah interacting protein, N terminal / SGS domain / SGS domain / SGS domain profile. / Protein S100-A6 / CS domain / CS domain ...Siah interacting protein, N-terminal / Calcyclin-binding protein, N-terminal / Calcyclin-binding Protein, CS domain / Siah interacting protein, N terminal / SGS domain / SGS domain / SGS domain profile. / Protein S100-A6 / CS domain / CS domain / CS domain profile. / HSP20-like chaperone / 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 / 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-A6 / Calcyclin-binding protein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsLee, Y. / Chazin, W.J.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of the S100A6 complex with a fragment from the C-terminal domain of Siah-1 interacting protein: a novel mode for S100 protein target recognition.
Authors: Lee, Y.T. / Dimitrova, Y.N. / Schneider, G. / Ridenour, W.B. / Bhattacharya, S. / Soss, S.E. / Caprioli, R.M. / Filipek, A. / Chazin, W.J.
History
DepositionAug 6, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A6
B: Protein S100-A6
C: Calcyclin-binding protein
D: Calcyclin-binding protein


Theoretical massNumber of molelcules
Total (without water)28,2284
Polymers28,2284
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 / 500structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein S100-A6 / S100 calcium-binding protein A6 / Calcyclin / Lung 10 kDa protein


Mass: 10167.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: S100A6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30801
#2: Protein/peptide Calcyclin-binding protein / CacyBP / Siah-interacting protein


Mass: 3946.425 Da / Num. of mol.: 2 / Fragment: S100A6 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cacybp, Sip / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CXW3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N NOESY
1313D HNCA
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HNCO
1732D 1H-13C HSQC
1833D (H)CCH-TOCSY
1933D 1H-13C NOESY
11043D 13C-filtered 15N-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE93% H2O/5% D2O/2% d-TFE
21 mM [U-100% 15N] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE93% H2O/5% D2O/2% d-TFE
31 mM [U-100% 13C] SIP(189-219), 1 mM S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 98% D2O/2% d-TFE98% D2O/2% d-TFE
42.3 mM [U-100% 13C] SIP(189-219), 2.3 mM [U-100% 15N] S100A6, 0.05 mM [U-2H] TRIS, 0.01 mM Ca2+, 93% H2O/5% D2O/2% d-TFE93% H2O/5% D2O/2% d-TFE
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSIP(189-219)[U-100% 13C; U-100% 15N]1
1 mMS100A61
0.05 mMTRIS[U-2H]1
0.01 mMCa2+1
1 mMSIP(189-219)[U-100% 15N]2
1 mMS100A62
0.05 mMTRIS[U-2H]2
0.01 mMCa2+2
1 mMSIP(189-219)[U-100% 13C]3
1 mMS100A63
0.05 mMTRIS[U-2H]3
0.01 mMCa2+3
2.3 mMSIP(189-219)[U-100% 13C]4
2.3 mMS100A6[U-100% 15N]4
0.05 mMTRIS[U-2H]4
0.01 mMCa2+4
Sample conditionsIonic strength: 0.08 / pH: 6.5 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE8004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 500 / Conformers submitted total number: 20

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