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- PDB-2zxx: Crystal structure of Cdt1/geminin complex -

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Basic information

Entry
Database: PDB / ID: 2zxx
TitleCrystal structure of Cdt1/geminin complex
Components
  • DNA replication factor Cdt1
  • Geminin
KeywordsCELL CYCLE/REPLICATION / COILED-COIL / Cell cycle / Coiled coil / DNA replication inhibitor / Phosphoprotein / DNA replication / DNA-binding / Nucleus / Proto-oncogene / Ubl conjugation / CELL CYCLE-REPLICATION COMPLEX
Function / homology
Function and homology information


Switching of origins to a post-replicative state / : / Activation of the pre-replicative complex / DNA-binding transcription factor binding => GO:0140297 / 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 ...Switching of origins to a post-replicative state / : / Activation of the pre-replicative complex / DNA-binding transcription factor binding => GO:0140297 / 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 / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / negative regulation of cell cycle / DNA polymerase binding / positive regulation of DNA replication / animal organ morphogenesis / kinetochore / histone deacetylase binding / transcription corepressor activity / mitotic cell cycle / protein-containing complex assembly / nuclear body / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Geminin / Geminin coiled-coil domain / CDT1 Geminin-binding domain-like / Geminin/Multicilin / DNA replication factor Cdt1 / Geminin / 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 ...Geminin / Geminin coiled-coil domain / CDT1 Geminin-binding domain-like / Geminin/Multicilin / DNA replication factor Cdt1 / Geminin / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Geminin / DNA replication factor Cdt1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsCho, Y. / Lee, C. / Hong, B.S. / Choi, J.M.
CitationJournal: Nature / Year: 2004
Title: Structural basis for inhibition of the replication licensing factor Cdt1 by geminin
Authors: Lee, C. / Hong, B.S. / Choi, J.M. / Kim, Y. / Watanabe, S. / Ishimi, Y. / Enomoto, T. / Tada, S. / Kim, Y. / Cho, Y.
History
DepositionJan 8, 2009Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 17, 2009ID: 1WLQ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geminin
B: Geminin
C: DNA replication factor Cdt1
D: Geminin
E: Geminin
F: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)84,0276
Polymers84,0276
Non-polymers00
Water1629
1
A: Geminin
B: Geminin
C: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)42,0133
Polymers42,0133
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-36 kcal/mol
Surface area20940 Å2
MethodPISA
2
D: Geminin
E: Geminin
F: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)42,0133
Polymers42,0133
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-39 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.769, 94.334, 115.572
Angle α, β, γ (deg.)90.00, 103.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Geminin /


Mass: 9466.405 Da / Num. of mol.: 4 / Fragment: Geminin coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: geminin, Gmnn / Plasmid: PET-28A, PACYC-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O88513
#2: Protein DNA replication factor Cdt1 / / Double parked homolog / DUP / Retroviral insertion site 2 protein


Mass: 23080.570 Da / Num. of mol.: 2 / Fragment: residues 172-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdt1 / Plasmid: PET-28A, PACYC-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8R4E9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorDetector: CCD / Date: Nov 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.787→112.509 Å / Num. all: 29821 / Num. obs: 28179
Reflection shellResolution: 2.8→2.9 Å / % possible all: 69.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.674 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.738 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27737 1432 5.1 %RANDOM
Rwork0.23495 ---
obs0.23715 26561 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.505 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å21.06 Å2
2--4.54 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 0 9 5476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9687495
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82624.43298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.916151078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4921550
X-RAY DIFFRACTIONr_chiral_restr0.1050.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024214
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.22849
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.23824
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9441.53400
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44825378
X-RAY DIFFRACTIONr_scbond_it2.06432401
X-RAY DIFFRACTIONr_scangle_it3.5224.52117
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 72 -
Rwork0.392 1356 -
obs--66.92 %

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