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- PDB-4ggc: Structural Analysis of Human Cdc20 Supports Multi-site Degron Rec... -

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Basic information

Entry
Database: PDB / ID: 4ggc
TitleStructural Analysis of Human Cdc20 Supports Multi-site Degron Recognition by APC/C
ComponentsCell division cycle protein 20 homologCell cycle
KeywordsCELL CYCLE / mitosis / securin / ubiquitination / WD40
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 mitotic metaphase/anaphase transition / positive regulation of synaptic plasticity / anaphase-promoting complex binding / 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 / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / 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 / protein ubiquitination / Ub-specific processing proteases / cell division / centrosome / nucleoplasm / cytosol
Similarity search - Function
The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Cell division cycle protein 20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLuo, X. / Tian, W. / Tomchick, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural analysis of human Cdc20 supports multisite degron recognition by APC/C.
Authors: Tian, W. / Li, B. / Warrington, R. / Tomchick, D.R. / Yu, H. / Luo, X.
#1: Journal: Mol.Cell / Year: 2007
Title: Cdc20: a WD40 activator for a cell cycle degradation machine
Authors: Yu, H.
#2: Journal: J.Biol.Chem. / Year: 2007
Title: KEN-box-dependent degradation of Bub1 spindle checkpoint kinase by the anaphase-promoting complex/cyclosome
Authors: Qi, W. / Yu, H.
#3: Journal: Dev.Cell / Year: 2001
Title: Mad2-independent inhibition of APC-Cdc20 by the mitotic checkpoint protein BubR1
Authors: Tang, Z. / Bharadwaj, R. / Li, B. / Yu, H.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3855
Polymers34,9121
Non-polymers4734
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.281, 86.933, 48.339
Angle α, β, γ (deg.)90.000, 112.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34912.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12834
#2: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES, 15% (w/v) PEG 6000, and 5% MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.35→28.117 Å / Num. all: 65746 / Num. obs: 65641 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 23.5
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.285 / Num. unique all: 2170 / % possible all: 63.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→28.117 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.93 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 13.54 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1464 3312 5.05 %RANDOM
Rwork0.1323 ---
all0.133 65641 --
obs0.133 65641 95.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.69 Å2 / Biso mean: 13.2412 Å2 / Biso min: 4.36 Å2
Refine analyzeLuzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.35→28.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 32 443 2897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082517
X-RAY DIFFRACTIONf_angle_d1.283440
X-RAY DIFFRACTIONf_chiral_restr0.074374
X-RAY DIFFRACTIONf_plane_restr0.007437
X-RAY DIFFRACTIONf_dihedral_angle_d13.639872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36930.1865910.17811700179163
1.3693-1.38970.1831990.17371918201770
1.3897-1.41140.17441070.17082174228180
1.4114-1.43460.1911040.15772385248987
1.4346-1.45930.1631530.16182485263893
1.4593-1.48580.16951390.15092640277998
1.4858-1.51440.16941410.147227522893100
1.5144-1.54530.18311300.132127052835100
1.5453-1.57890.15081520.127327082860100
1.5789-1.61570.16421720.125227142886100
1.6157-1.65610.13271500.122627132863100
1.6561-1.70080.14491500.119226852835100
1.7008-1.75090.12621360.123227052841100
1.7509-1.80740.14731500.124627382888100
1.8074-1.8720.13241450.124927142859100
1.872-1.94690.15951410.125427262867100
1.9469-2.03550.13681430.123227162859100
2.0355-2.14280.16581500.123627122862100
2.1428-2.27690.14521420.124927412883100
2.2769-2.45270.15321370.127427192856100
2.4527-2.69930.14571520.132627362888100
2.6993-3.08950.14861410.137127302871100
3.0895-3.89080.11531410.129127442885100
3.8908-28.12260.14131460.138627692915100
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)
10.036-0.01110.03160.16120.00190.0833-0.0354-0.06420.0511-0.0090.0310.0084-0.0256-0.0479-0.00010.06410.0027-0.00020.0749-0.00460.0714-9.4626-8.760719.131
20.14250.0204-0.08430.0959-0.06030.083-0.0333-0.1769-0.11840.05010.0512-0.0438-0.0089-0.09360.00650.06480.01040.00160.11820.00520.0409-5.4638-18.191728.7233
30.0046-0.0055-0.00540.1360.03460.05990.0301-0.16-0.00290.23020.0206-0.05940.057-0.00670.01410.14150.00330.00970.09110.03170.049-2.4776-26.884730.5731
40.3808-0.0912-0.04450.23010.0060.280.02240.0328-0.0217-0.0392-0.0169-0.01410.0304-0.008800.0579-0.0032-0.0020.0464-0.00110.0533-0.8023-22.54417.0105
50.1352-0.12130.01750.14320.0140.07080.0302-0.00270.0469-0.0085-0.031-0.0058-0.0292-0.04520.00270.05990.00360.00240.0618-0.00360.0776-11.2211-5.720710.6451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 202 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 245 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 265 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 266 through 418 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 419 through 477 )A0

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