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- PDB-2rqq: Structure of C-terminal region of Cdt1 -

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Basic information

Entry
Database: PDB / ID: 2rqq
TitleStructure of C-terminal region of Cdt1
ComponentsDNA replication factor Cdt1
KeywordsCELL CYCLE / licensing factor / DNA replication / DNA-binding / Proto-oncogene
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 / attachment of mitotic spindle microtubules to kinetochore ...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 / attachment of mitotic spindle microtubules to kinetochore / DNA replication checkpoint signaling / 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 / simulated annealing
Model detailsclosest to the average, model 1
AuthorsJee, J.G. / Mizuno, T. / Kamada, K. / Tochio, H. / Hiroaki, H. / Hanaoka, F. / Shirakawa, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins
Authors: Jee, J.G. / Mizuno, T. / Kamada, K. / Tochio, H. / Chiba, Y. / Yanagi, K. / Yasuda, G. / Hiroaki, H. / Hanaoka, F. / Shirakawa, M.
History
DepositionOct 14, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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)12,7521
Polymers12,7521
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 lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 12751.950 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 450-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdt1, Ris2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R4E9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 1mM [U-99% 13C; U-99% 15N] protein; 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: entity-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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