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- PDB-4n14: Crystal structure of Cdc20 and apcin complex -

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Basic information

Entry
Database: PDB / ID: 4n14
TitleCrystal structure of Cdc20 and apcin complex
ComponentsCell division cycle protein 20 homolog
KeywordsCELL CYCLE/CELL CYCLE INHIBITOR / cell cycle / mitosis / securin / ubiquitination / WD40 / CELL CYCLE-CELL CYCLE INHIBITOR complex
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 / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of synapse maturation / 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 / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of synapse maturation / 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 / ubiquitin ligase activator activity / positive regulation of mitotic metaphase/anaphase transition / 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 / ubiquitin-like ligase-substrate adaptor activity / 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 / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / 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 pole / spindle / 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
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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-WR7 / Cell division cycle protein 20 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLuo, X. / Tian, W. / Yu, H.
Citation
Journal: Nature / Year: 2014
Title: Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C.
Authors: Sackton, K.L. / Dimova, N. / Zeng, X. / Tian, W. / Zhang, M. / Sackton, T.B. / Meaders, J. / Pfaff, K.L. / Sigoillot, F. / Yu, H. / Luo, X. / King, R.W.
#1: Journal: Mol.Cell / Year: 2007
Title: Cdc20: a WD40 activator for a cell cycle degradation machine.
Authors: Yu, H.
History
DepositionOct 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 5, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 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)34,8762
Polymers34,4381
Non-polymers4391
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.041, 87.177, 48.043
Angle α, β, γ (deg.)90.000, 112.720, 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: 34437.559 Da / Num. of mol.: 1 / Fragment: WD domain residues 165-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC20 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12834
#2: Chemical ChemComp-WR7 / 2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl [(1R)-2,2,2-trichloro-1-(pyrimidin-2-ylamino)ethyl]carbamate / apcin


Mass: 438.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H14Cl3N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
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: Jun 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: 2.1→28.58 Å / Num. all: 16859 / Num. obs: 16859 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.082 / Χ2: 1.299 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.981.20.552800.586124.4
1.98-2.021.20.3733690.542134.4
2.02-2.061.40.5244650.533141.3
2.06-2.11.50.4135690.71152.2
2.1-2.151.70.3856920.663160.8
2.15-2.21.90.367950.632173.3
2.2-2.252.30.3949350.644182.7
2.25-2.312.70.3969460.704187.8
2.31-2.3830.36810670.738193
2.38-2.463.30.33710650.737196.9
2.46-2.543.60.31411080.814199.6
2.54-2.653.80.2611160.8261100
2.65-2.7740.21211130.9241100
2.77-2.9140.17111300.9821100
2.91-3.14.10.13111061.204199.8
3.1-3.334.10.10211131.501199.9
3.33-3.6740.08211211.873199.6
3.67-4.23.90.07211052.2861100
4.2-5.293.90.05811302.3881100
5.29-503.90.04711511.789199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.58 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.2 / σ(F): 0 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 857 5.08 %RANDOM
Rwork0.1653 ---
all0.1678 16859 --
obs0.1678 16859 92.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.8 Å2 / Biso mean: 33.0041 Å2 / Biso min: 10.31 Å2
Refine analyzeLuzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 27 81 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022526
X-RAY DIFFRACTIONf_angle_d0.7343452
X-RAY DIFFRACTIONf_chiral_restr0.044372
X-RAY DIFFRACTIONf_plane_restr0.003442
X-RAY DIFFRACTIONf_dihedral_angle_d13.442877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.23150.29061000.21371915201567
2.2315-2.40380.27861450.20872563270889
2.4038-2.64550.24661370.19022855299299
2.6455-3.02790.2141480.179428683016100
3.0279-3.81350.2071550.153629053060100
3.8135-28.58440.18471720.14428963068100
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)
10.0858-0.00020.02530.2961-0.0140.204-0.0358-0.08090.1623-0.0238-0.0248-0.0263-0.0571-0.002200.1201-0.0035-0.00450.1207-0.03710.1492-27.6683-11.324267.3995
20.093-0.15050.05870.2722-0.03480.05920.1041-0.1705-0.11340.2878-0.0363-0.06840.10640.09760.02090.213-0.0196-0.0190.18580.02520.1452-20.5382-25.221572.642
30.6635-0.1041-0.3750.3842-0.00340.85330.01480.0556-0.0658-0.124-0.0284-0.07470.11590.0429-0.00060.1345-0.0302-0.00740.0956-0.02070.1112-19.2153-23.399251.1549
40.2476-0.1733-0.06660.16560.00170.1575-0.04490.00510.1962-0.0094-0.0695-0.02-0.2466-0.1534-0.00070.1875-0.0026-0.03980.1663-0.01110.2034-29.543-6.681955.143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 221 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 222 through 265 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 266 through 418 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 419 through 477 )A0

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