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- PDB-5jja: Crystal structure of a PP2A B56gamma/BubR1 complex -

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Basic information

Entry
Database: PDB / ID: 5jja
TitleCrystal structure of a PP2A B56gamma/BubR1 complex
Components
  • Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
KeywordsSIGNALING PROTEIN / PP2A / BubR1 / B56gamma
Function / homology
Function and homology information


mitotic checkpoint complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / protein phosphatase regulator activity / outer kinetochore / protein localization to chromosome, centromeric region ...mitotic checkpoint complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / metaphase/anaphase transition of mitotic cell cycle / protein phosphatase regulator activity / outer kinetochore / protein localization to chromosome, centromeric region / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Platelet sensitization by LDL / CTLA4 inhibitory signaling / mitotic spindle assembly checkpoint signaling / protein phosphatase activator activity / chromosome, centromeric region / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / RAF activation / Degradation of beta-catenin by the destruction complex / kinetochore / spindle / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Regulation of TP53 Degradation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of cell population proliferation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Mad3/Bub1 homology region 1 / Mitotic spindle checkpoint protein Bub1/Mad3 / Mad3/BUB1 homology region 1 / BUB1 N-terminal domain profile. / Mad3/BUB1 hoMad3/BUB1 homology region 1 / Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWang, Z. / Wang, J. / Rao, Z. / Xu, W.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
Chinese Academy of SciencesXDB08010303 China
CitationJournal: Protein Cell / Year: 2016
Title: Crystal structure of a PP2A B56-BubR1 complex and its implications for PP2A substrate recruitment and localization.
Authors: Wang, J. / Wang, Z. / Yu, T. / Yang, H. / Virshup, D.M. / Kops, G.J. / Lee, S.H. / Zhou, W. / Li, X. / Xu, W. / Rao, Z.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
C: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta
D: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)98,7334
Polymers98,7334
Non-polymers00
Water4,324240
1
A: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
C: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)49,3672
Polymers49,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-4 kcal/mol
Surface area17000 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
D: Mitotic checkpoint serine/threonine-protein kinase BUB1 beta


Theoretical massNumber of molelcules
Total (without water)49,3672
Polymers49,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.017, 95.588, 167.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform / PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61- ...PP2A B subunit isoform B'-gamma / PP2A B subunit isoform B56-gamma / PP2A B subunit isoform PR61-gamma / PP2A B subunit isoform R5-gamma / Renal carcinoma antigen NY-REN-29


Mass: 41366.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R5C, KIAA0044 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13362
#2: Protein Mitotic checkpoint serine/threonine-protein kinase BUB1 beta / MAD3/BUB1-related protein kinase / hBUBR1 / Mitotic checkpoint kinase MAD3L / Protein SSK1


Mass: 7999.618 Da / Num. of mol.: 2 / Mutation: S670D, S676D, T680D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BUB1B, BUBR1, MAD3L, SSK1 / Production host: Escherichia coli (E. coli)
References: UniProt: O60566, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.53 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5 and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 54953 / % possible obs: 100 % / Redundancy: 10.5 % / Net I/σ(I): 24.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JAK

2jak


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.913 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.161
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 2882 5 %RANDOM
Rwork0.1795 ---
obs0.1807 54953 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.44 Å2 / Biso mean: 44.293 Å2 / Biso min: 26.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---1.69 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 0 240 5927
Biso mean---43.66 -
Num. residues----682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195843
X-RAY DIFFRACTIONr_bond_other_d0.0010.025708
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9777923
X-RAY DIFFRACTIONr_angle_other_deg0.755313171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7775676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56424.036275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.727151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0611529
X-RAY DIFFRACTIONr_chiral_restr0.0610.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
X-RAY DIFFRACTIONr_mcbond_it1.3143.0872722
X-RAY DIFFRACTIONr_mcbond_other1.3133.0852721
X-RAY DIFFRACTIONr_mcangle_it2.2234.6113392
LS refinement shellResolution: 2.361→2.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 218 -
Rwork0.224 3984 -
all-4202 -
obs--98.66 %
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)
12.9711-0.12241.57870.32470.04191.18580.0018-0.0696-0.10790.12940.01370.04410.0342-0.0218-0.01550.0542-0.00260.02060.0284-0.01780.031189.111718.276115.8956
20.8515-1.2125-0.38173.50741.49451.21520.0724-0.0173-0.1652-0.1119-0.10910.21210.1353-0.02940.03670.0854-0.0041-0.00150.021-0.00870.051189.8474-18.3336-26.2469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 375
2X-RAY DIFFRACTION2B30 - 376

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