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- PDB-9i6a: Crystal structure of human Cdc20 bound to synthetic D-box peptide D7 -

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Basic information

Entry
Database: PDB / ID: 9i6a
TitleCrystal structure of human Cdc20 bound to synthetic D-box peptide D7
Components
  • ALA-PRO-0JY-GLY
  • 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 / regulation of dendrite development / Inactivation of APC/C via direct inhibition of the APC/C complex ...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 / regulation of dendrite development / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / positive regulation of synaptic plasticity / Phosphorylation of Emi1 / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / anaphase-promoting complex binding / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator 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 / histone deacetylase binding / spindle pole / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / cell differentiation / Ub-specific processing proteases / protein ubiquitination / cell division / positive regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / 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: 1.915 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: ALA-PRO-0JY-GLY


Theoretical massNumber of molelcules
Total (without water)55,7542
Polymers55,7542
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-3 kcal/mol
Surface area11620 Å2
Unit cell
Length a, b, c (Å)35.003, 86.869, 48.027
Angle α, β, γ (deg.)90.00, 109.60, 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 ALA-PRO-0JY-GLY


Mass: 957.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: D-box peptide with non-natural amino acid / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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 XE 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: 1.915→45.243 Å / Num. obs: 14979 / % possible obs: 71.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.064 / Rrim(I) all: 0.147 / Net I/σ(I): 7.6 / Num. measured all: 76640
Reflection shellResolution: 1.915→2.094 Å / % possible obs: 15.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 1.161 / Num. measured all: 3657 / Num. unique obs: 750 / Rpim(I) all: 0.573 / Rrim(I) all: 1.299 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.915→45.24 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.883 / SU R Cruickshank DPI: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.288 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.199
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 774 5.17 %RANDOM
Rwork0.2065 ---
obs0.2078 14966 71.8 %-
Displacement parametersBiso mean: 29.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.0908 Å20 Å20.9019 Å2
2--6.3739 Å20 Å2
3----3.2831 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 1.915→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 9 72 2437
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082429HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13321HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d784SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes411HARMONIC5
X-RAY DIFFRACTIONt_it2429HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.2
X-RAY DIFFRACTIONt_other_torsion15.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2161SEMIHARMONIC4
LS refinement shellResolution: 1.92→2.05 Å / Total num. of bins used: 39
RfactorNum. reflection% reflection
Rfree0.2109 -5.58 %
Rwork0.2066 372 -
all0.2068 394 -
obs--10.57 %
Refinement TLS params.Method: refined / Origin x: -1.4037 Å / Origin y: -15.5029 Å / Origin z: 14.7136 Å
111213212223313233
T-0.1446 Å2-0.0294 Å20.0058 Å2-0.0027 Å2-0.0117 Å2---0.1163 Å2
L1.1271 °2-0.2656 °2-0.1579 °2-0.9059 °2-0.1113 °2--2.9423 °2
S-0.0706 Å °-0.0081 Å °0.0024 Å °0.0257 Å °0.0269 Å °-0.0325 Å °0.0009 Å °0.0706 Å °0.0437 Å °
Refinement TLS groupSelection details: { A|* }

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