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- PDB-2fv4: NMR solution structure of the yeast kinetochore Spc24/Spc25 globu... -

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Basic information

Entry
Database: PDB / ID: 2fv4
TitleNMR solution structure of the yeast kinetochore Spc24/Spc25 globular domain
Components
  • Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region
  • Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING / alpha-beta / complex / coiled-coil
Function / homology
Function and homology information


centromere clustering / Ndc80 complex / sister chromatid biorientation / outer kinetochore / chromosome segregation / kinetochore / cell division / identical protein binding / nucleus
Similarity search - Function
Double Stranded RNA Binding Domain - #430 / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinetochore protein SPC25 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsSchnell, J.R. / Chou, J.J.
CitationJournal: Structure / Year: 2006
Title: Structure of a central component of the yeast kinetochore: the spc24p/spc25p globular domain.
Authors: Wei, R.R. / Schnell, J.R. / Larsen, N.A. / Sorger, P.K. / Chou, J.J. / Harrison, S.C.
History
DepositionJan 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4May 29, 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: Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region
B: Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region


Theoretical massNumber of molelcules
Total (without water)19,5122
Polymers19,5122
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical 25.2 kDa protein in AFG3-SEB2 intergenic region


Mass: 10585.985 Da / Num. of mol.: 1 / Fragment: SPC25P GLOBULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YER018C / Plasmid: PET3ATR / Cell line (production host): ROSETTA / Production host: Escherichia coli (E. coli) / References: UniProt: P40014
#2: Protein Hypothetical 24.6 kDa protein in ILV2-ADE17 intergenic region


Mass: 8926.170 Da / Num. of mol.: 1 / Fragment: SPC24P GLOBULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YMR117C, YM9718.16C / Plasmid: PET3ATR / Cell line (production host): ROSETTA / Production host: Escherichia coli (E. coli) / References: UniProt: Q04477

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TROSY versions of HNCA, HN(CA)CB and HNCO; 3D 15N-TOCSY-HSQC.
122TROSY versions of HNCA, HN(CA)CB and HNCO; 3D 15N-TOCSY-HSQC.
1333D 15N-NOESY, 3D 13C-NOESY, and 3D 15N-edited 13C-filtered NOESY; 2D spin echo difference experiments for measuring three-bond J(C'C) and J(NC); standard HNCO-based 3D experiments for measuring one-bond J(NH) and J(C'CA).
1443D 15N-NOESY, 3D 13C-NOESY, and 3D 15N-edited 13C-filtered NOESY; 2D spin echo difference experiments for measuring three-bond J(C'C), J(NC) and J(CC); standard HNCO-based 3D experiments for measuring one-bond J(NH).
155Standard HNCO-based 3D experiments for measuring residual one-bond D(NH) and D(C'CA).
166Standard HNCO-based 3D experiments for measuring residual one-bond D(NH).

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM spc25G U-15N,13C,85%-2H, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.
21.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C,85%-2H, 95% H2O, 5% D2O50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.
31.5 mM spc25G U-15N,13C, 1.5 mM spc24G natural abundance isotopes, 95% H2O, 5% D2O50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.
41.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 95% H2O, 5% D2O50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.
51.5 mM spc25G U-15N,13C, 85%-2H, 1.5 mM spc24G natural abundance isotopes, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.
61.5 mM spc25G natural abundance isotopes, 1.5 mM spc24G U-15N,13C, 50 mg/mL Pf1 phage, 95% H2O, 5% D2O50 mM Phosphate buffer Na, pH 7.0, 1 mM azide, 95% H2O, 5% D2O.
Sample conditionsIonic strength: 50 mM sodium phosphate buffer / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Frank Delaglioprocessing
CARA1.2Rochus Kellerdata analysis
Xplor-NIH2.11Charles Schwietersrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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