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

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Basic information

Entry
Database: PDB / ID: 4gga
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 / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / 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 / spindle / kinetochore / 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 / molecular replacement / Resolution: 2.044 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 21, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)46,3511
Polymers46,3511
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.865, 87.258, 110.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46350.996 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM Na citrate, 15 % (w/v) PEG 6000, and 4% MPD, pH 5.6, 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: Apr 18, 2010 / 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: 2.044→68.589 Å / Num. all: 25867 / Num. obs: 24684 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 18.7 Å2 / Limit h max: 19 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 54 / Limit l min: 0 / Rmerge(I) obs: 0.222 / Net I/σ(I): 10
Reflection scaleGroup code: 1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.599 / Num. unique all: 1044 / % possible all: 83.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1062refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.044→38.347 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.41 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1239 5.02 %RANDOM
Rwork0.151 ---
all0.1536 24766 --
obs0.1536 -95.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.81 Å2 / Biso mean: 23.3523 Å2 / Biso min: 3.56 Å2
Refine analyzeLuzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.044→38.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 0 247 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112509
X-RAY DIFFRACTIONf_angle_d1.3273429
X-RAY DIFFRACTIONf_chiral_restr0.08373
X-RAY DIFFRACTIONf_plane_restr0.006441
X-RAY DIFFRACTIONf_dihedral_angle_d13.338872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.0444-2.12630.2321230.179222312354223184
2.1263-2.22310.23891290.17623832512238389
2.2231-2.34020.27331280.177125152643251594
2.3402-2.48680.23521340.176326202754262097
2.4868-2.67880.24871410.162626722813267299
2.6788-2.94830.20331430.158826872830268799
2.9483-3.37470.20911430.146727072850270799
3.3747-4.25090.16991440.121627432887274399
4.2509-38.35360.15941540.140528773031287799
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)
10.2550.12490.02270.48710.25470.2412-0.0452-0.14410.00830.17520.0527-0.04750.01620.0148-0.00060.07050.0238-0.00320.0853-0.01240.0338-15.407-15.50229.8225
20.1754-0.1508-0.07550.13580.01370.1828-0.0369-0.0221-0.0437-0.02630.0108-0.07310.06340.022500.0842-0.01720.00510.07190.00430.0754-9.9054-27.132514.1041
30.2609-0.12480.09760.361-0.00290.1201-0.022-0.01550.0515-0.0325-0.00110.0243-0.037-0.0418-0.00070.0447-0.00250.00060.0446-0.02110.0585-21.8168-9.466411.3438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 277 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 278 through 359 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 360 through 478 )A0

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