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- PDB-4rg9: Crystal structure of APC3-APC16 complex (Selenomethionine Derivative) -

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Basic information

Entry
Database: PDB / ID: 4rg9
TitleCrystal structure of APC3-APC16 complex (Selenomethionine Derivative)
Components
  • Anaphase-promoting complex subunit 16
  • Cell division cycle protein 27 homolog
KeywordsPROTEIN BINDING / Asymmetric complex / TPR folding / Protein assembly
Function / homology
Function and homology information


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 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination ...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 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / 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 / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / protein ubiquitination / cell division / centrosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsYamaguchi, M. / Yu, S. / Miller, D.J. / Schulman, B.A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structure of an APC3-APC16 Complex: Insights into Assembly of the Anaphase-Promoting Complex/Cyclosome.
Authors: Yamaguchi, M. / Yu, S. / Qiao, R. / Weissmann, F. / Miller, D.J. / VanderLinden, R. / Brown, N.G. / Frye, J.J. / Peters, J.M. / Schulman, B.A.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division cycle protein 27 homolog
B: Cell division cycle protein 27 homolog
S: Anaphase-promoting complex subunit 16


Theoretical massNumber of molelcules
Total (without water)134,0813
Polymers134,0813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-34 kcal/mol
Surface area41060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.019, 116.019, 184.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 3 / APC3 / CDC27 homolog / CDC27Hs / H-NUC


Mass: 64455.441 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-180, 447-824
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P30260
#2: Protein/peptide Anaphase-promoting complex subunit 16 / APC16 / Cyclosome subunit 16


Mass: 5170.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC16, C10orf104 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96DE5

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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: 4.63 Å3/Da / Density % sol: 73.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M MES, pH 6.2, 0.24M magnesium chloride, 6% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 38356 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Rsym value: 0.125
Reflection shellResolution: 3.25→3.39 Å / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXmodel building
REFMAC5.8.0049refinement
pointlessdata scaling
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.25→49.94 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 20.298 / SU ML: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.954 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24846 1813 5 %RANDOM
Rwork0.20971 ---
obs0.21166 34309 94.21 %-
all-38356 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.504 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2--2.14 Å20 Å2
3----4.28 Å2
Refinement stepCycle: LAST / Resolution: 3.25→49.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 0 0 7542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197720
X-RAY DIFFRACTIONr_bond_other_d0.0060.026970
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.95510486
X-RAY DIFFRACTIONr_angle_other_deg0.788315940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32224.057350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.891151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6251532
X-RAY DIFFRACTIONr_chiral_restr0.060.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021861
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9318.3973905
X-RAY DIFFRACTIONr_mcbond_other2.9318.3963904
X-RAY DIFFRACTIONr_mcangle_it4.89912.5794869
X-RAY DIFFRACTIONr_mcangle_other4.89812.584870
X-RAY DIFFRACTIONr_scbond_it3.8398.3713815
X-RAY DIFFRACTIONr_scbond_other3.8388.3723816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.54812.5045617
X-RAY DIFFRACTIONr_long_range_B_refined8.1167.269095
X-RAY DIFFRACTIONr_long_range_B_other8.1167.2659096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 112 -
Rwork0.336 2217 -
obs--82.3 %

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