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- PDB-1r21: Solution Structure of human Ki67 FHA Domain -

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Basic information

Entry
Database: PDB / ID: 1r21
TitleSolution Structure of human Ki67 FHA Domain
ComponentsAntigen Ki-67
KeywordsCELL CYCLE / beta sandwich
Function / homology
Function and homology information


regulation of chromosome segregation / regulation of chromatin organization / regulation of mitotic nuclear division / chromosome / cell population proliferation / nuclear body / cell cycle / nucleolus / DNA binding / RNA binding ...regulation of chromosome segregation / regulation of chromatin organization / regulation of mitotic nuclear division / chromosome / cell population proliferation / nuclear body / cell cycle / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
KI67R / KI67R (NUC007) repeat / K167/Chmadrin repeat / Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...KI67R / KI67R (NUC007) repeat / K167/Chmadrin repeat / Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Proliferation marker protein Ki-67
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsByeon, I.J. / Li, H. / Tsai, M.D.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of Human Ki67 FHA Domain and its Binding to a Phosphoprotein Fragment from hNIFK Reveal Unique Recognition Sites and New Views to the Structural Basis of FHA Domain Functions
Authors: Li, H. / Byeon, I.J. / Ju, Y. / Tsai, M.D.
History
DepositionSep 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antigen Ki-67


Theoretical massNumber of molelcules
Total (without water)14,5561
Polymers14,5561
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 100structures with the lowest energy,target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Antigen Ki-67 / cell proliferation antigen Ki-67 / long form / antigen identified by monoclonal antibody Ki-67 / ...cell proliferation antigen Ki-67 / long form / antigen identified by monoclonal antibody Ki-67 / Proliferation-related Ki-67 antigen


Mass: 14555.519 Da / Num. of mol.: 1 / Fragment: FHA domain / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: nucleusCell nucleus / Gene: MKI67 / Plasmid: pEG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P46013

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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
2323D 13C-separated NOESY
2423D 15N-separated NOESY
1532D NOESY
1642D NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM U-13C,15N-protein; 10 mM TrisHCl buffer (pH 8.4); 2mM DTT; 1 mM EDTA95% H2O, 10% D2O
20.5 mM U-13C,15N-protein; 5 mM HEPES buffer (pH 7.5); 2mM DTT; 1 mM EDTA; 150 mM NaCl95% H2O, 10% D2O
30.5 mM unlabeled-protein; 10 mM TrisHCl buffer (pH 8.4); 2mM DTT; 1 mM EDTA95% H2O, 10% D2O
40.5 mM unlabeled-protein; 10 mM TrisHCl buffer (pH 8.4); 2mM DTT; 1 mM EDTA100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 8.4 ambient 290 K
2150 mM NaCl 7.5 ambient 290 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
X-PLORNIH versionBrunger,Schwieters, Kuszewski, Tjandra, Clorestructure solution
X-PLORNIH versionBrunger,Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1921 constraints: 1694 from NOE, 62 from H-bonding, 165 from dihedral angle constraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 23

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