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- PDB-2klo: Structure of the Cdt1 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2klo
TitleStructure of the Cdt1 C-terminal domain
ComponentsDNA replication factor Cdt1
KeywordsCELL CYCLE / mouse Cdt1 / replication licensing factor / winged helix fold / mcm binding / DNA replication / DNA-binding / Nucleus / Phosphoprotein / Proto-oncogene / Ubl conjugation
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Activation of the pre-replicative complex / DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / regulation of nuclear cell cycle DNA replication / negative regulation of DNA-templated DNA replication / DNA replication checkpoint signaling ...Switching of origins to a post-replicative state / Activation of the pre-replicative complex / DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / regulation of nuclear cell cycle DNA replication / negative regulation of DNA-templated DNA replication / DNA replication checkpoint signaling / attachment of mitotic spindle microtubules to kinetochore / regulation of DNA-templated DNA replication initiation / DNA polymerase binding / kinetochore / mitotic cell cycle / nuclear body / chromatin binding / DNA binding / nucleus
Similarity search - Function
DNA replication factor Cdt1, C-terminal WH domain / CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...DNA replication factor Cdt1, C-terminal WH domain / CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA replication factor Cdt1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, molecular dynamics, TORSION ANGLE DYNAMICS
Model detailslowest energy, model 1
AuthorsKhayrutdinov, B.I. / Bae, W.J. / Yun, Y.M. / Tsuyama, T. / Kim, J.J. / Hwang, E. / Ryu, K.-S. / Cheong, H.-K. / Cheong, C. / Karplus, P.A. ...Khayrutdinov, B.I. / Bae, W.J. / Yun, Y.M. / Tsuyama, T. / Kim, J.J. / Hwang, E. / Ryu, K.-S. / Cheong, H.-K. / Cheong, C. / Karplus, P.A. / Guntert, P. / Tada, S. / Jeon, Y.H. / Cho, Y.
CitationJournal: Protein Sci. / Year: 2009
Title: Structure of the Cdt1 C-terminal domain: Conservation of the winged helix fold in replication licensing factors
Authors: Khayrutdinov, B.I. / Bae, W.J. / Yun, Y.M. / Lee, J.H. / Tsuyama, T. / Kim, J.J. / Hwang, E. / Ryu, K.-S. / Cheong, H.-K. / Cheong, C. / Ko, J.-S. / Enomoto, T. / Karplus, P.A. / Guntert, P. ...Authors: Khayrutdinov, B.I. / Bae, W.J. / Yun, Y.M. / Lee, J.H. / Tsuyama, T. / Kim, J.J. / Hwang, E. / Ryu, K.-S. / Cheong, H.-K. / Cheong, C. / Ko, J.-S. / Enomoto, T. / Karplus, P.A. / Guntert, P. / Tada, S. / Jeon, Y.H. / Cho, Y.
History
DepositionJul 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)15,5451
Polymers15,5451
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA replication factor Cdt1 / Double parked homolog / DUP / Retroviral insertion site 2 protein


Mass: 15545.268 Da / Num. of mol.: 1 / Fragment: C-terminal domain, UNP residues 420-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdt1, Ris2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R4E9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D CBCA(CO)NH
1313D CACBNH
1413D HN(CA)CO
1513D HNCO
1613D HN(CO)CA
1713D HNCA
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D C(CCO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11313D CCH-TOCSY
11413D 1H-13C NOESY

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Sample preparation

DetailsContents: 20mM MES-1, 80mM sodium chloride-2, 10mM beta-mercaptoethanol-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMMES-11
80 mMsodium chloride-21
10 mMbeta-mercaptoethanol-31
Sample conditionsIonic strength: 80 / pH: 6.8 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
OPALLuginbuhl, Guntert, Billeter and Wuthrichstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, molecular dynamics, TORSION ANGLE DYNAMICS
Software ordinal: 1
NMR constraintsNOE constraints total: 3295 / NOE long range total count: 371 / NOE medium range total count: 473 / NOE sequential total count: 2451
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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