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- PDB-2wvr: Human Cdt1:Geminin complex -

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Basic information

Entry
Database: PDB / ID: 2wvr
TitleHuman Cdt1:Geminin complex
Components
  • DNA REPLICATION FACTOR CDT1
  • GEMININ
KeywordsREPLICATION / DNA REPLICATION LICENSE / DNA REPLICATION INHIBITOR / PHOSPHOPROTEIN / UBL CONJUGATION / DNA REPLICATION / DNA-BINDING / POLYMORPHISM / PROTO-ONCOGENE / NUCLEUS / CELL CYCLE / ACETYLATION / COILED COIL
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / regulation of DNA replication origin binding / Switching of origins to a post-replicative state / 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 ...DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / regulation of DNA replication origin binding / Switching of origins to a post-replicative state / 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 / G1/S-Specific Transcription / negative regulation of DNA replication / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex / DNA polymerase binding / regulation of mitotic cell cycle / transcription repressor complex / positive regulation of DNA replication / Assembly of the pre-replicative complex / animal organ morphogenesis / kinetochore / Orc1 removal from chromatin / histone deacetylase binding / transcription corepressor activity / mitotic cell cycle / DNA-binding transcription factor binding / nuclear body / cell division / negative regulation of DNA-templated transcription / chromatin binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsDe Marco, V. / Perrakis, A.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Quaternary structure of the human Cdt1-Geminin complex regulates DNA replication licensing.
Authors: V De Marco / P J Gillespie / A Li / N Karantzelis / E Christodoulou / R Klompmaker / S van Gerwen / A Fish / M V Petoukhov / M S Iliou / Z Lygerou / R H Medema / J J Blow / D I Svergun / S ...Authors: V De Marco / P J Gillespie / A Li / N Karantzelis / E Christodoulou / R Klompmaker / S van Gerwen / A Fish / M V Petoukhov / M S Iliou / Z Lygerou / R H Medema / J J Blow / D I Svergun / S Taraviras / A Perrakis /
Abstract: All organisms need to ensure that no DNA segments are rereplicated in a single cell cycle. Eukaryotes achieve this through a process called origin licensing, which involves tight spatiotemporal ...All organisms need to ensure that no DNA segments are rereplicated in a single cell cycle. Eukaryotes achieve this through a process called origin licensing, which involves tight spatiotemporal control of the assembly of prereplicative complexes (pre-RCs) onto chromatin. Cdt1 is a key component and crucial regulator of pre-RC assembly. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent DNA rereplication. Here, we address the mechanism of DNA licensing inhibition by Geminin, by combining X-ray crystallography, small-angle X-ray scattering, and functional studies in Xenopus and mammalian cells. Our findings show that the Cdt1:Geminin complex can exist in two distinct forms, a "permissive" heterotrimer and an "inhibitory" heterohexamer. Specific Cdt1 residues, buried in the heterohexamer, are important for licensing. We postulate that the transition between the heterotrimer and the heterohexamer represents a molecular switch between licensing-competent and licensing-defective states.
History
DepositionOct 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GEMININ
B: GEMININ
C: DNA REPLICATION FACTOR CDT1


Theoretical massNumber of molelcules
Total (without water)107,7343
Polymers107,7343
Non-polymers00
Water0
1
A: GEMININ
B: GEMININ
C: DNA REPLICATION FACTOR CDT1

A: GEMININ
B: GEMININ
C: DNA REPLICATION FACTOR CDT1


Theoretical massNumber of molelcules
Total (without water)215,4686
Polymers215,4686
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14450 Å2
ΔGint-98.5 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.804, 92.804, 164.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsTHE BIOLOGICAL UNIT IS A DIMER OF THE AU TRIMER, HETEROHEXAMER, CONFIRMED BY SAXS MEASUREMENTS.

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Components

#1: Protein GEMININ /


Mass: 23598.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET27/46 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: O75496
#2: Protein DNA REPLICATION FACTOR CDT1 / / CDT1 / DOUBLE PARKED HOMOLOG / DUP


Mass: 60537.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET27/46 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2 / References: UniProt: Q9H211

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 72 % / Description: NONE
Crystal growpH: 7.5 / Details: PH 7.5 100-150 MM NACL CAPILLARY GRADIENT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.065
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.065 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. obs: 11298 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 136.48 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.9
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.3→19.413 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 32.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3007 529 4.7 %
Rwork0.2403 --
obs0.2433 11298 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 108 Å2
Baniso -1Baniso -2Baniso -3
1--14.8671 Å2-0 Å20 Å2
2---14.8671 Å2-0 Å2
3---29.7342 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 0 0 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042661
X-RAY DIFFRACTIONf_angle_d0.793579
X-RAY DIFFRACTIONf_dihedral_angle_d19.2381047
X-RAY DIFFRACTIONf_chiral_restr0.053379
X-RAY DIFFRACTIONf_plane_restr0.006472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3004-3.63060.34721280.31612622X-RAY DIFFRACTION100
3.6306-4.15150.40021320.26432643X-RAY DIFFRACTION100
4.1515-5.21360.28471320.23572684X-RAY DIFFRACTION100
5.2136-19.41370.2761370.22132820X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.25850.0998-0.0989-0.0282-0.2611-0.658-0.16380.41290.2703-0.0877-0.0050.0057-0.67620.784-0.3328-0.85950.53220.585-0.06410.02-0.112525.7491-6.0105-12.2287
22.0363-0.52570.17081.53431.56791.78430.87020.7325-1.09790.1153-0.93180.68371.0599-0.92931.2458-0.7499-0.61380.1551-0.6913-0.6222-0.269922.4529-26.38168.0581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR CHAIN B
2X-RAY DIFFRACTION2CHAIN C

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