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- PDB-2k2i: NMR Solution structure of the C-terminal domain (T94-Y172) of the... -

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Basic information

Entry
Database: PDB / ID: 2k2i
TitleNMR Solution structure of the C-terminal domain (T94-Y172) of the human centrin 2 in complex with a repeat sequence of human Sfi1 (R641-T660)
Components
  • Centrin-2
  • SFI1 peptide
KeywordsCELL CYCLE / Centrin 2 / Sfi1 / Human / Cell division / Mitosis / Phosphoprotein
Function / homology
Function and homology information


XPC complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / transcription export complex 2 / nuclear pore nuclear basket / sperm principal piece / centriole replication / phosphatase binding / SUMOylation of DNA damage response and repair proteins / mRNA export from nucleus ...XPC complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / transcription export complex 2 / nuclear pore nuclear basket / sperm principal piece / centriole replication / phosphatase binding / SUMOylation of DNA damage response and repair proteins / mRNA export from nucleus / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / centriole / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / sperm midpiece / AURKA Activation by TPX2 / regulation of cytokinesis / nucleotide-excision repair / microtubule cytoskeleton organization / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / apical part of cell / Formation of Incision Complex in GG-NER / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / protein transport / ciliary basal body / spermatogenesis / microtubule binding / cell division / centrosome / calcium ion binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / : / ATP-dependent RNA helicase DEAD-box, conserved site / EF-hand domain pair / 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
Similarity search - Domain/homology
Protein SFI1 homolog / Centrin-2 / Protein SFI1 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMartinez-Sanz, J. / Assairi, L. / Blouquit, Y. / Duchambon, P. / Mouawad, L. / Craescu, C.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure, dynamics and thermodynamics of the human centrin 2/hSfi1 complex
Authors: Martinez-Sanz, J. / Kateb, F. / Assairi, L. / Blouquit, Y. / Bodenhausen, G. / Abergel, D. / Mouawad, L. / Craescu, C.T.
History
DepositionApr 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 1, 2015Group: Atomic model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrin-2
B: SFI1 peptide


Theoretical massNumber of molelcules
Total (without water)11,6162
Polymers11,6162
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)15 / 500
RepresentativeModel #1closest to the average

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Components

#1: Protein Centrin-2 / Caltractin isoform 1


Mass: 9234.317 Da / Num. of mol.: 1 / Fragment: UNP residues 94-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CETN2, CALT, CEN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41208
#2: Protein/peptide SFI1 peptide


Mass: 2381.695 Da / Num. of mol.: 1 / Fragment: UNP residues 610-629 / Source method: obtained synthetically
Details: The peptide is chemically synthesized. It is found naturally in humans.
Source: (synth.) Homo sapiens (human) / References: UniProt: Q5W1B5, UniProt: A8K8P3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D DQF-COSY
1332D 1H-1H TOCSY
1432D 1H-1H NOESY
1523D HNCA
1623D HN(CO)CA
1713D 1H-15N NOESY
1813D 1H-15N TOCSY
1942D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] C-HsCen2, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] C-HsCen2, 95% H2O/5% D2O95% H2O/5% D2O
31 mM C-HsCen2, 95% H2O/5% D2O95% H2O/5% D2O
41 mM C-HsCen2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-HsCen2[U-100% 15N]1
1 mMC-HsCen2[U-100% 13C; U-100% 15N]2
1 mMC-HsCen23
1 mMC-HsCen24
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000.1Accelrys, inc.chemical shift assignment
Felix2000.1Accelrys, inc.peak picking
Discover_molecular_modeling_system2.98Accelrys Inc.data analysis
Discover_molecular_modeling_system2.98Accelrys Inc.geometry optimization
Discover_molecular_modeling_system2.98Accelrys Inc.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers calculated total number: 500 / Conformers submitted total number: 15

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