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- PDB-9i68: Crystal structure of human Cdc20 bound to synthetic D-box peptide D21 -

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Basic information

Entry
Database: PDB / ID: 9i68
TitleCrystal structure of human Cdc20 bound to synthetic D-box peptide D21
Components
  • ARG-ALA-PRO-3EG-SER-ASP
  • Cell division cycle protein 20 homolog
KeywordsLIGASE / APC/C / degron / D-box
Function / homology
Function and homology information


metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins ...metaphase/anaphase transition of cell cycle / metaphase/anaphase transition of meiosis I / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of anaphase-promoting complex-dependent catabolic process / regulation of meiotic nuclear division / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / anaphase-promoting complex binding / positive regulation of mitotic metaphase/anaphase transition / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / mitotic spindle assembly / ubiquitin-like ligase-substrate adaptor activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Resolution of Sister Chromatid Cohesion / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RHO GTPases Activate Formins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / kinetochore / spindle / spindle pole / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / cell differentiation / Ub-specific processing proteases / protein ubiquitination / cell division / centrosome / nucleoplasm / cytosol
Similarity search - Function
: / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cell division cycle protein 20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.505 Å
AuthorsEapen, R. / Okoye, C. / Stubbs, C. / Schimpl, M. / Tischer, T. / Fisher, E.J. / Zacharopoulou, M. / Ferrer, F. / Barford, D. / Spring, D. ...Eapen, R. / Okoye, C. / Stubbs, C. / Schimpl, M. / Tischer, T. / Fisher, E.J. / Zacharopoulou, M. / Ferrer, F. / Barford, D. / Spring, D. / Lindon, C. / Phillips, C. / Itzhaki, L.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R004137/1 United Kingdom
CitationJournal: To be published
Title: Development of D-box peptides to inhibit the Anaphase Promoting Complex/Cyclosome
Authors: Eapen, R. / Okoye, C. / Stubbs, C. / Schimpl, M. / Tischer, T. / Fisher, E.J. / Zacharopoulou, M. / Ferrer, F. / Barford, D. / Spring, D. / Lindon, C. / Phillips, C. / Itzhaki, L.S.
History
DepositionJan 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle protein 20 homolog
B: ARG-ALA-PRO-3EG-SER-ASP


Theoretical massNumber of molelcules
Total (without water)55,8102
Polymers55,8102
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-0 kcal/mol
Surface area12310 Å2
Unit cell
Length a, b, c (Å)35.491, 87.550, 48.573
Angle α, β, γ (deg.)90.00, 109.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cell division cycle protein 20 homolog / p55CDC


Mass: 54796.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12834
#2: Protein/peptide ARG-ALA-PRO-3EG-SER-ASP


Mass: 1013.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 10 % MPD, 12-14 % PEG 6000, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.505→45.73 Å / Num. obs: 32820 / % possible obs: 74.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Rrim(I) all: 0.056 / Net I/σ(I): 13.1
Reflection shellResolution: 1.509→1.666 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.598 / Num. unique obs: 1641 / Rpim(I) all: 0.333 / Rrim(I) all: 0.688

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
Aimlessdata scaling
STARANISOdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.505→45.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.093
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 1602 4.88 %RANDOM
Rwork0.1752 ---
obs0.1761 32820 74.2 %-
Displacement parametersBiso mean: 25.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.3677 Å20 Å20.7586 Å2
2--1.6778 Å20 Å2
3----1.3101 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.505→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 9 236 2670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013531HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d840SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it2574HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.22
X-RAY DIFFRACTIONt_other_torsion15.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion325SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2273SEMIHARMONIC4
LS refinement shellResolution: 1.505→1.6 Å
RfactorNum. reflection% reflection
Rfree0.2327 -4.26 %
Rwork0.2086 629 -
obs--8.6 %
Refinement TLS params.Method: refined / Origin x: -1.5267 Å / Origin y: -15.8789 Å / Origin z: 14.6791 Å
111213212223313233
T-0.0829 Å2-0.0377 Å20.0077 Å2--0.0364 Å2-0.0194 Å2---0.06 Å2
L0.9589 °2-0.0993 °2-0.2671 °2-0.6599 °20.0225 °2--2.3955 °2
S-0.0611 Å °-0.0086 Å °-0.0085 Å °0.0008 Å °0.0323 Å °-0.0186 Å °-0.0112 Å °0.1262 Å °0.0289 Å °
Refinement TLS groupSelection details: { A|* }

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