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- PDB-4ggd: Structural analysis of human Cdc20 supports multisite degron reco... -

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Basic information

Entry
Database: PDB / ID: 4ggd
TitleStructural analysis of human Cdc20 supports multisite degron recognition by APC/C.
Components
  • Cell division cycle protein 20 homolog
  • Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
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 / positive regulation of synapse maturation / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of dendrite development / meiotic sister chromatid cohesion, centromeric ...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 / positive regulation of synapse maturation / regulation of meiotic nuclear division / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of dendrite development / meiotic sister chromatid cohesion, centromeric / 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 / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex binding / protein localization to chromosome, centromeric region / outer kinetochore / 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 / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / 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 / non-specific serine/threonine protein kinase / protein kinase activity / Ub-specific processing proteases / protein ubiquitination / ciliary basal body / cell division / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / centrosome / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 4 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / 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 / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / Cell division cycle protein 20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.435 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 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.5Feb 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
B: Cell division cycle protein 20 homolog
C: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
D: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)100,5134
Polymers100,5134
Non-polymers00
Water3,333185
1
A: Cell division cycle protein 20 homolog
C: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)50,2562
Polymers50,2562
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division cycle protein 20 homolog
D: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)50,2562
Polymers50,2562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.826, 88.129, 118.351
Angle α, β, γ (deg.)90.000, 99.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 47495.273 Da / Num. of mol.: 2
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: Protein/peptide Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / MAD3/BUB1-related protein kinase / hBUBR1 / Mitotic checkpoint kinase MAD3L / Protein SSK1


Mass: 2761.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: O60566, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: sitting-drop vapor diffusion / pH: 9.3
Details: 50 mM CAPSO, 5% (w/v) PEG 6000, and 15.5 % MPD, pH 9.3, sitting-drop vapor diffusion, 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: Oct 17, 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: 2.435→48.6 Å / Num. all: 36956 / Num. obs: 36910 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 39.4 Å2 / Limit h max: 19 / Limit h min: -20 / Limit k max: 35 / Limit k min: 0 / Limit l max: 47 / Limit l min: 0 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.7
Reflection scaleGroup code: 1
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.9 % / Num. unique all: 1762 / % possible all: 93.4

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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: 2.435→29.168 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 1835 4.97 %RANDOM
Rwork0.1541 ---
all0.1565 36910 --
obs0.1565 36910 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.68 Å2 / Biso mean: 43.9021 Å2 / Biso min: 8.96 Å2
Refine analyzeLuzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.435→29.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 0 185 5134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135079
X-RAY DIFFRACTIONf_angle_d1.4176928
X-RAY DIFFRACTIONf_chiral_restr0.077757
X-RAY DIFFRACTIONf_plane_restr0.006888
X-RAY DIFFRACTIONf_dihedral_angle_d14.4241766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.4346-2.50040.261110.215922412352224180
2.5004-2.57390.30071460.205827142860271499
2.5739-2.65690.24461490.195726932842269397
2.6569-2.75180.26271400.18827142854271498
2.7518-2.86190.26761410.184726942835269499
2.8619-2.9920.24581420.180327002842270098
2.992-3.14960.22521470.169627462893274698
3.1496-3.34670.2091330.166627282861272899
3.3467-3.60460.21941410.149627492890274999
3.6046-3.96660.18511460.141827442890274499
3.9666-4.53870.16881440.119127712915277199
4.5387-5.71130.15521510.119727542905275499
5.7113-29.170.17571440.161328272971282799
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)
10.49950.39220.13560.76630.19520.3115-0.0590.30760.43310.0775-0.00660.0443-0.08220.0917-0.31620.19620.0542-0.03410.31810.18150.2692-12.146312.2023-55.5632
20.1266-0.3356-0.01950.92890.05720.4171-0.00440.3202-0.110.01120.07590.30670.1944-0.22-0.01090.1338-0.0132-0.05650.3386-0.02150.1469-21.9958-1.6915-54.7155
30.16920.0239-0.01940.0698-0.0830.09610.0698-0.0833-0.26560.10890.0220.04440.0378-0.02760.00030.18830.0069-0.00270.1357-0.00210.169-8.7197-8.182-41.4999
40.32010.1116-0.07630.2671-0.08510.1264-0.10090.26550.42440.1764-0.0919-0.1818-0.07880.1791-0.01510.21080.0103-0.03260.21830.10680.3259-0.846810.1311-49.1967
50.4101-0.2844-0.14390.81510.31270.680.0185-0.4593-0.2651-0.0274-0.08270.1015-0.037-0.1553-0.44010.1071-0.05880.05460.28580.14010.1575-3.5612-8.4054-2.3752
60.34540.1409-0.0940.2031-0.17250.1968-0.0639-0.05380.1114-0.0525-0.03390.066-0.0542-0.01-00.1256-0.01610.00210.1075-0.03180.13474.77183.8902-13.63
70.1803-0.0147-0.05750.1173-0.07030.3430.0113-0.2729-0.521-0.0903-0.0941-0.21930.13680.27070.05990.193-0.03820.05240.21070.25230.369113.5664-14.0262-8.1723
80.0009-0.00010.00140.0020.00120.00250.0255-0.0077-0.00220.01340.02750.02830.02380.012500.48670.1405-0.02360.4271-0.16190.3447-14.91310.6371-33.9571
90.00360.0012-0.00160.0004-0.00030.00060.01630.03580.02810.00720.09430.02760.04510.0032-00.2912-0.06990.00550.1836-0.01920.2185-1.4582-12.5557-24.7615
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 285 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 359 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 476 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 165 through 254 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 255 through 380 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 381 through 476 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 5 through 11 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 4 through 11 )D0

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