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

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Basic information

Entry
Database: PDB / ID: 5bpz
TitleAtomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain
ComponentsAnapc5 protein
KeywordsCELL CYCLE / Apc5 / APC/C / anaphase promoting complex
Function / homology
Function and homology information


anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / protein K11-linked ubiquitination / spindle / cell division / cytoplasm
Similarity search - Function
: / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Armadillo-type fold
Similarity search - Domain/homology
Anaphase-promoting complex subunit 5
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsCronin, N. / Yang, J. / Zhang, Z. / Barford, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC576/A14109 United Kingdom
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

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Assembly

Deposited unit
A: Anapc5 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5783
Polymers19,4541
Non-polymers1242
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint7 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.972, 57.297, 63.616
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Anapc5 protein


Mass: 19453.600 Da / Num. of mol.: 1 / Fragment: N-terminus, UNP residues 1-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: anapc5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q0IH16
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 46.53 % / Description: Blocks
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: The protein was concentrated to 3.4 mg/mL. Plate-like crystals were grown in a buffer containing 40 mM sodium propionate, 20 mM sodium cacodylate, 40 mM Bis-Tris propane (pH 7.0) and 25% ...Details: The protein was concentrated to 3.4 mg/mL. Plate-like crystals were grown in a buffer containing 40 mM sodium propionate, 20 mM sodium cacodylate, 40 mM Bis-Tris propane (pH 7.0) and 25% PEG1500. Larger crystals were obtained by seeding.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0081 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 2.18→63.63 Å / Num. all: 8213 / Num. obs: 8213 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 28.5
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 4.5 / Num. unique all: 590 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementResolution: 2.18→63 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.9208 / SU R Cruickshank DPI: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.303 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 395 4.93 %RANDOM
Rwork0.2113 ---
obs0.2122 8007 99.63 %-
Displacement parametersBiso max: 145.33 Å2 / Biso mean: 59.49 Å2 / Biso min: 27.89 Å2
Baniso -1Baniso -2Baniso -3
1-12.047 Å20 Å20 Å2
2---12.5723 Å20 Å2
3---0.5253 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: final / Resolution: 2.18→63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 14 48 1200
Biso mean--62.52 58.68 -
Num. residues----133
LS refinement shellResolution: 2.2→2.46 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2759 113 5.13 %
Rwork0.2304 2090 -
all0.2327 2203 -
obs--99.63 %
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)
16.8401-3.54290.47781.42311.16411.30270.0337-0.21660.2715-0.0627-0.0086-0.2161-0.0978-0.1025-0.025-0.13670.01590.03320.00330.0476-0.061231.45639.962613.3105
210.0196-0.48311.24593.5715-0.52183.73890.0781-0.815-0.7339-0.11910.08380.04420.0722-0.1284-0.162-0.20820.0175-0.0086-0.10790.0656-0.102824.194210.337314.3409
38.78962.90754.65482.12112.10645.06890.1484-1.1351-0.04040.104-0.1076-0.1123-0.0827-0.0899-0.0408-0.23880.0426-0.00040.2170.0193-0.138922.731514.592420.9746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|29 - A|58 }A29 - 58
2X-RAY DIFFRACTION2{ A|59 - A|117 }A59 - 117
3X-RAY DIFFRACTION3{ A|118 - A|168 }A118 - 168

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