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- PDB-4rg7: Crystal structure of APC3 -

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Basic information

Entry
Database: PDB / ID: 4rg7
TitleCrystal structure of APC3
ComponentsCell division cycle protein 27 homologCell cycle
KeywordsPROTEIN BINDING / Symmetric homodimer / 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 / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / 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 / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / 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 / mitotic spindle / spindle / CDK-mediated phosphorylation and removal of Cdc6 / 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, cyclosome, subunit 3 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Cell division cycle protein 27 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.25 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: 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


Theoretical massNumber of molelcules
Total (without water)127,7852
Polymers127,7852
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-24 kcal/mol
Surface area41940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.408, 118.408, 273.739
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell division cycle protein 27 homolog / Cell cycle / 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

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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: 4.34 Å3/Da / Density % sol: 71.63 %
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: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.25→50 Å / Num. obs: 15458 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rsym value: 0.119
Reflection shellResolution: 4.25→4.4 Å / Rsym value: 0.826 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.25→49.666 Å / SU ML: 0.68 / σ(F): 1.35 / Phase error: 33.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 765 5.03 %RANDOM
Rwork0.2548 ---
obs0.256 15211 99.57 %-
all-15458 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.25→49.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6066 0 0 0 6066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056192
X-RAY DIFFRACTIONf_angle_d1.2438529
X-RAY DIFFRACTIONf_dihedral_angle_d13.4091748
X-RAY DIFFRACTIONf_chiral_restr0.0461005
X-RAY DIFFRACTIONf_plane_restr0.0051137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.25-4.57840.34151490.30032883X-RAY DIFFRACTION100
4.5784-5.03870.30221660.29922866X-RAY DIFFRACTION100
5.0387-5.76690.33671490.32622874X-RAY DIFFRACTION99
5.7669-7.2620.34971670.30082900X-RAY DIFFRACTION100
7.262-49.6690.21361340.19862923X-RAY DIFFRACTION99
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)
15.59860.6198-0.287210.10921.56769.31870.0357-0.68771.25840.1160.1915-0.56120.81941.1704-0.30870.9909-0.2181-0.09811.4355-0.14371.027718.97318.1707-18.3317
24.1435-1.2008-1.04946.38-1.08097.55840.03580.1597-0.3243-0.9223-0.0206-0.34850.26531.112-0.40421.31060.04630.00371.2124-0.16170.91999.0705-3.1276-21.8179
35.29411.4481-2.63987.19690.99757.21850.37840.33010.5967-0.8846-0.6728-0.9814-0.3904-0.83780.25681.33720.14670.29641.2754-0.00241.2459-3.0629-9.6692-4.4089
46.5531-2.45163.68784.4447-4.17273.5675-0.0994-0.67260.27790.370.10460.55950.0832-0.5166-0.10941.05310.04660.05371.0281-0.12320.9272-14.56555.2026-3.1976
57.4924-0.25213.20212.63261.24265.76680.28390.76470.10030.2387-0.18060.39721.2795-1.014-0.07281.3035-0.3538-0.06871.15740.07260.9295-20.62495.5922-20.5426
66.6519-5.8086.09347.2905-7.44987.30853.5432-1.8345-0.6062-1.6216-0.91394.63953.2393-3.8501-1.90692.4389-0.8484-0.63742.27840.00872.8525-35.0659-10.9288-22.227
74.7553-1.9091-0.17027.2999-1.53459.2696-1.3248-0.23940.0804-0.42771.0114-0.19122.2878-1.4215-0.21331.73-0.2239-0.27511.51380.09951.3607-27.8214-20.8828-12.8248
86.4056-0.8572-3.37446.01533.71386.5182-0.1036-0.3126-0.225-0.5642-0.18150.7407-0.7560.91440.33031.17780.0674-0.17660.8597-0.22821.0718.57099.08260.1078
92.85740.3575-2.57578.1682-1.84794.4352-0.4444-1.75291.55181.17110.78630.234-3.51122.9773-0.44112.3415-0.80330.00232.1223-0.1821.339114.436928.86378.7961
100.28330.8517-0.40252.6876-0.70930.12170.15690.43490.74520.9812-0.6343-0.6402-0.65030.4930.04191.5078-0.47910.43362.3266-0.25661.222424.857636.3088-2.0344
119.04650.7469-0.83934.7382-0.62465.84060.05160.37440.9174-0.4565-0.0592-1.0112-1.13710.6589-0.10981.7478-0.6427-0.08761.6781-0.00351.437925.156641.0441-17.4064
125.942-2.0932-0.54924.80741.79245.6153-0.14770.19630.5746-1.02610.54081.7499-0.7949-0.0361-0.27732.2136-0.2831-0.19521.4950.26432.0814.103546.7599-17.087
135.50640.0808-3.52172.6995-4.81251.97892.8246-0.13762.902-0.37361.36721.6579-4.9013-2.3138-3.43472.7614-0.08230.08931.61040.60454.23267.468869.5805-13.8028
148.6830.9102-4.82186.0750.14439.05011.898-2.1852.74351.01290.42521.2146-3.87052.4613-1.26492.6031-0.53130.66562.0423-0.54733.064421.632869.0848-15.7528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:92 )A5 - 92
2X-RAY DIFFRACTION2( CHAIN A AND RESID 93:171 )A93 - 171
3X-RAY DIFFRACTION3( CHAIN A AND RESID 464:504 )A464 - 504
4X-RAY DIFFRACTION4( CHAIN A AND RESID 505:572 )A505 - 572
5X-RAY DIFFRACTION5( CHAIN A AND RESID 573:687 )A573 - 687
6X-RAY DIFFRACTION6( CHAIN A AND RESID 688:738 )A688 - 738
7X-RAY DIFFRACTION7( CHAIN A AND RESID 739:774 )A739 - 774
8X-RAY DIFFRACTION8( CHAIN B AND RESID 6:81 )B6 - 81
9X-RAY DIFFRACTION9( CHAIN B AND RESID 82:144 )B82 - 144
10X-RAY DIFFRACTION10( CHAIN B AND RESID 145:171 )B145 - 171
11X-RAY DIFFRACTION11( CHAIN B AND RESID 465:534 )B465 - 534
12X-RAY DIFFRACTION12( CHAIN B AND RESID 535:686 )B535 - 686
13X-RAY DIFFRACTION13( CHAIN B AND RESID 687:724 )B687 - 724
14X-RAY DIFFRACTION14( CHAIN B AND RESID 725:774 )B725 - 774

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