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- PDB-4rg6: Crystal structure of APC3-APC16 complex -

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Basic information

Entry
Database: PDB / ID: 4rg6
TitleCrystal structure of APC3-APC16 complex
Components
  • Anaphase-promoting complex subunit 16
  • Cell division cycle protein 27 homolog
KeywordsPROTEIN BINDING / Asymmetric complex / TPR fplding / 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 / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C ...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 / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic 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 / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / regulation of mitotic cell cycle / 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 / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / spindle / neuron projection development / mitotic 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 / MOLECULAR REPLACEMENT / Resolution: 3.3 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: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
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 27 homolog
B: Cell division cycle protein 27 homolog
S: Anaphase-promoting complex subunit 16


Theoretical massNumber of molelcules
Total (without water)132,8623
Polymers132,8623
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-30 kcal/mol
Surface area41660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.660, 116.660, 184.972
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: 63892.691 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: 5076.753 Da / Num. of mol.: 1 / Fragment: UNP residues 74-109
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

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, pH 6.0, 0.2M magnesium chloride, 8% 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-C / Wavelength: 1.0716 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 37171 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.1
Reflection shellResolution: 3.3→3.42 Å / Rsym value: 0.829 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 19.124 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.853 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24241 1867 5 %RANDOM
Rwork0.2033 ---
obs0.20525 35265 99.76 %-
all-37171 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 102.696 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å20 Å2
2--3.82 Å20 Å2
3----7.65 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7598 0 0 0 7598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197775
X-RAY DIFFRACTIONr_bond_other_d0.0060.027061
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.94810550
X-RAY DIFFRACTIONr_angle_other_deg0.789316170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7485975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98224.153354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.938151222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0981532
X-RAY DIFFRACTIONr_chiral_restr0.0590.21160
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021865
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_it4.24610.6953921
X-RAY DIFFRACTIONr_mcbond_other4.24310.6943920
X-RAY DIFFRACTIONr_mcangle_it6.86416.0274889
X-RAY DIFFRACTIONr_mcangle_other6.86416.0284890
X-RAY DIFFRACTIONr_scbond_it3.95410.6643854
X-RAY DIFFRACTIONr_scbond_other3.95310.6653855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.53315.9385661
X-RAY DIFFRACTIONr_long_range_B_refined9.95185.3519216
X-RAY DIFFRACTIONr_long_range_B_other9.9585.3589217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 149 -
Rwork0.29 2544 -
obs--99.48 %

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