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- PDB-2aff: The solution structure of the Ki67FHA/hNIFK(226-269)3P complex -

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Basic information

Entry
Database: PDB / ID: 2aff
TitleThe solution structure of the Ki67FHA/hNIFK(226-269)3P complex
Components
  • Antigen KI-67
  • MKI67 FHA domain interacting nucleolar phosphoprotein
KeywordsCELL CYCLE / Ki67 / FHA / NIFK / NMR / Phosphoprotein
Function / homology
Function and homology information


regulation of chromosome segregation / regulation of chromatin organization / regulation of mitotic nuclear division / rRNA metabolic process / rRNA transcription / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / condensed nuclear chromosome / chromosome / protein-containing complex assembly / cell population proliferation ...regulation of chromosome segregation / regulation of chromatin organization / regulation of mitotic nuclear division / rRNA metabolic process / rRNA transcription / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / condensed nuclear chromosome / chromosome / protein-containing complex assembly / cell population proliferation / nuclear body / cell cycle / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
KI67R / KI67R (NUC007) repeat / K167/Chmadrin repeat / Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding / FHA Ki67 binding domain of hNIFK / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain ...KI67R / KI67R (NUC007) repeat / K167/Chmadrin repeat / Protein phosphatase 1 binding domain / Protein phosphatase 1 binding / MKI67 FHA domain-interacting nucleolar phosphoprotein, FHA Ki67 binding / FHA Ki67 binding domain of hNIFK / 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 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Proliferation marker protein Ki-67 / MKI67 FHA domain-interacting nucleolar phosphoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Li, H. / Song, H. / Gronenborn, A.M. / Tsai, M.D.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Sequential phosphorylation and multisite interactions characterize specific target recognition by the FHA domain of Ki67.
Authors: Byeon, I.J. / Li, H. / Song, H. / Gronenborn, A.M. / Tsai, M.D.
#1: Journal: 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.L. / Ju, Y. / Tsai, M.-D.
History
DepositionJul 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen KI-67
B: MKI67 FHA domain interacting nucleolar phosphoprotein


Theoretical massNumber of molelcules
Total (without water)19,0242
Polymers19,0242
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)100 / 512structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Antigen KI-67


Mass: 13826.766 Da / Num. of mol.: 1 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus: Escherichia / Gene: MKI67 / Plasmid: PEG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46013
#2: Protein/peptide MKI67 FHA domain interacting nucleolar phosphoprotein / Nucleolar protein interacting with the FHA domain of pKI-67 / hNIFK / Nucleolar phosphoprotein Nopp34


Mass: 5197.442 Da / Num. of mol.: 1 / Fragment: residues 226-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus: Escherichia / Gene: MKI67IP / Plasmid: pEG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BYG3

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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
1333D 13C-separated NOESY
1433D 15N-separated NOESY
1513D 12C/14N-filtered 13C separated NOESY
1633D 12C/14N-filtered 13C separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM Ki67 FHA U-15N,13C; 1 mM hNIFK(226-269)3P unlabeled 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.493% H2O/7% D2O
20.9 mM Ki67 FHA U-15N,13C; 1 mM hNIFK(226-269)3P unlabeled 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.4100% D2O
31 mM Ki67 FHA unlabled; 0.9 mM hNIFK(226-269)3P U-15N,13C 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.493% H2O/7% D2O
41 mM Ki67 FHA unlabled; 0.9 mM hNIFK(226-269)3P U-15N,13C 5 mM HEPES, 5 mM DTT, 1 mM EDTA, 150 mM NaCl, pH 7.4100% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX7502
Bruker AVANCEBrukerAVANCE6003
Bruker DMXBrukerDMX5004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH versionBrungerstructure solution
X-PLORNIH versionBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 3476 constraints, 3141 are distance, 215 dihedral angle, and 120 N-H residual dipolar coupling constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 512 / Conformers submitted total number: 100

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