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

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Basic information

Entry
Database: PDB / ID: 5bpt
TitleAtomic-resolution structures of the APC/C subunits Apc4 and the Apc5 N-terminal domain
ComponentsMGC81278 protein
KeywordsCELL CYCLE / Apc4 / APC/C / anaphase promoting complex
Function / homology
Function and homology information


anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / nuclear periphery / cell division
Similarity search - Function
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 speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 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 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: MGC81278 protein


Theoretical massNumber of molelcules
Total (without water)85,4151
Polymers85,4151
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 area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.469, 90.469, 115.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein MGC81278 protein / Apc4


Mass: 85415.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: anapc4, MGC81278 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6NU36
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Apc4 was concentrated to 3.5 mg/ml in a buffer of 20 mM Hepes (pH 8.0), 200 mM NaCl and 2 mM DTT. Initial crystal was obtained by vapour diffusion in setting drop in a buffer containing 0.1 ...Details: Apc4 was concentrated to 3.5 mg/ml in a buffer of 20 mM Hepes (pH 8.0), 200 mM NaCl and 2 mM DTT. Initial crystal was obtained by vapour diffusion in setting drop in a buffer containing 0.1 M sodium citrate 5.0, 8% (w/v) PEG 8K. By seeding with the initial crystals, large crystals were grown in a buffer containing 0.1 M sodium citrate 5.0, 3% (w/v) PEG 8K, 250 mM magnesium acetate, 10 mM Tris.HCl (pH 8.5), 200 mM NDSB-211, 4% (v/v) ethylene glycol and 2 mM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 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: 0.969 Å / Relative weight: 1
ReflectionResolution: 3.2→29.3 Å / Num. all: 15477 / Num. obs: 15477 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 107.57 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 13.3
Reflection shellResolution: 3.2→3.47 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER-TNT2.10.1refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
BUSTER2.11.4refinement
RefinementMethod to determine structure: MAD / Resolution: 3.2→48.71 Å / Cor.coef. Fo:Fc: 0.9131 / Cor.coef. Fo:Fc free: 0.8692 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.451
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 1016 6.59 %RANDOM
Rwork0.2227 ---
obs0.2254 15414 99.99 %-
Displacement parametersBiso max: 266.66 Å2 / Biso mean: 107.87 Å2 / Biso min: 49.75 Å2
Baniso -1Baniso -2Baniso -3
1-4.4769 Å20 Å20 Å2
2--4.4769 Å20 Å2
3----8.9538 Å2
Refine analyzeLuzzati coordinate error obs: 0.83 Å
Refinement stepCycle: final / Resolution: 3.2→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 0 0 4786
Num. residues----614
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1707SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes692HARMONIC5
X-RAY DIFFRACTIONt_it4871HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion656SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5378SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4871HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6601HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion21.85
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2625 162 5.85 %
Rwork0.2527 2605 -
all0.2533 2767 -
obs--99.99 %
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)
12.66590.07480.37422.2608-0.19041.1056-0.052-0.345-0.57980.5559-0.00390.42320.007-0.01610.0559-0.10420.03280.3073-0.1336-0.05660.006718.09721.667510.0612
21.85670.4016-0.39320.87790.37932.5770.0106-0.6093-0.26140.3945-0.33110.1285-0.1455-0.22150.32050.14030.11220.16180.13490.0233-0.235338.424326.9234.2636
32.75630.72260.52982.6629-0.70542.3639-0.20310.6031-0.4719-0.03930.10330.84460.3584-0.15010.0998-0.2895-0.0330.1971-0.1357-0.3270.13378.774121.8539-11.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|231}A2 - 231
2X-RAY DIFFRACTION2{ A|232 - A|530}A232 - 530
3X-RAY DIFFRACTION3{ A|531 - A|740}A531 - 740

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