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- PDB-5bpw: Atomic-resolution structures of the APC/C subunits Apc4 and the A... -

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Basic information

Entry
Database: PDB / ID: 5bpw
TitleAtomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain
ComponentsAnaphase-promoting complex subunit 4
KeywordsCELL CYCLE / Apc4 / APC/C / anaphase promoting complex
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 / regulation of meiotic 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 / protein branched polyubiquitination / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / 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 / nuclear periphery / 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 / CDK-mediated phosphorylation and removal of Cdc6 / ubiquitin-protein transferase activity / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / cell division / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Anaphase-promoting complex subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsKulkarni, K. / Yang, J. / Zhang, Z. / Barford, D.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Atomic-Resolution Structures of the APC/C Subunits Apc4 and the Apc5 N-Terminal Domain.
Authors: Cronin, N.B. / Yang, J. / Zhang, Z. / Kulkarni, K. / Chang, L. / Yamano, H. / Barford, D.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anaphase-promoting complex subunit 4


Theoretical massNumber of molelcules
Total (without water)95,9601
Polymers95,9601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.181, 139.181, 156.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Anaphase-promoting complex subunit 4 / APC4 / Cyclosome subunit 4


Mass: 95960.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX5

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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: 4.36 Å3/Da / Density % sol: 71.76 % / Description: Thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Apc4 crystals were grown by vapour-diffusion in a buffer containing 10 mM malic acid, 20 mM MES, 20 mM Tris.HCl (pH 8.0), 160 mM NDSB 196, 10 mM EDTA and 19% (v/v) PEG 1500. Crystals were ...Details: Apc4 crystals were grown by vapour-diffusion in a buffer containing 10 mM malic acid, 20 mM MES, 20 mM Tris.HCl (pH 8.0), 160 mM NDSB 196, 10 mM EDTA and 19% (v/v) PEG 1500. Crystals were incubated in a cryoprotection buffer comprising 10 mM malic acid, 20 mM MES, 20 mM Tris.HCl (pH 8.0), 160 mM NDSB 196, 10 mM EDTA, 22% (v/v) PEG 1500 and 20% (v/v) ethylene glycol prior to freezing in liquid nitrogen.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.4→57.8 Å / Num. all: 21671 / Num. obs: 21671 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.182 / Net I/σ(I): 5.16
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / Num. measured obs: 4371 / Num. unique all: 4371 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 3.4→51.943 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2749 700 3.24 %
Rwork0.2201 20931 -
obs0.2208 21631 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 217 Å2 / Biso mean: 91.8312 Å2 / Biso min: 41.32 Å2
Refinement stepCycle: final / Resolution: 3.4→51.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5091 0 0 0 5091
Num. residues----659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125183
X-RAY DIFFRACTIONf_angle_d1.8287025
X-RAY DIFFRACTIONf_chiral_restr0.074833
X-RAY DIFFRACTIONf_plane_restr0.008878
X-RAY DIFFRACTIONf_dihedral_angle_d16.971854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4001-3.66250.36221280.2874088421699
3.6625-4.0310.311460.247441074253100
4.031-4.61390.26251420.203541384280100
4.6139-5.81180.2291360.193542244360100
5.8118-51.94920.27551480.2144374452299

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