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- PDB-6oyl: The structure of the PP2A B56 subunit KIF4A complex -

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Basic information

Entry
Database: PDB / ID: 6oyl
TitleThe structure of the PP2A B56 subunit KIF4A complex
Components
  • Chromosome-associated kinesin KIF4A
  • Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
KeywordsHYDROLASE / Ser/thr phosphatase / complex
Function / homology
Function and homology information


microtubule motor activity => GO:0003777 / organelle organization / mitotic spindle midzone assembly / protein phosphatase type 2A complex / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / anterograde axonal transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...microtubule motor activity => GO:0003777 / organelle organization / mitotic spindle midzone assembly / protein phosphatase type 2A complex / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / anterograde axonal transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / 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 / Kinesins / Disassembly of the destruction complex and recruitment of AXIN to the membrane / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / CTLA4 inhibitory signaling / Platelet sensitization by LDL / microtubule-based movement / iron-sulfur cluster binding / protein phosphatase activator activity / Recycling pathway of L1 / mitotic cytokinesis / 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 / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / mitotic spindle organization / RHO GTPases Activate Formins / RAF activation / spindle microtubule / Degradation of beta-catenin by the destruction complex / nuclear matrix / Negative regulation of MAPK pathway / Separation of Sister Chromatids / antigen processing and presentation of exogenous peptide antigen via MHC class II / Regulation of TP53 Degradation / chromosome / midbody / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / microtubule binding / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of cell population proliferation / Golgi apparatus / signal transduction / DNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Protein phosphatase 2A, regulatory B subunit, B56 / Protein phosphatase 2A regulatory B subunit (B56 family) / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Kinesin motor domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Chromosome-associated kinesin KIF4A / 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: 3.15 Å
AuthorsWang, X. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS091336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Elife / Year: 2020
Title: A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment.
Authors: Wang, X. / Garvanska, D.H. / Nasa, I. / Ueki, Y. / Zhang, G. / Kettenbach, A.N. / Peti, W. / Nilsson, J. / Page, R.
History
DepositionMay 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
B: Chromosome-associated kinesin KIF4A


Theoretical massNumber of molelcules
Total (without water)46,6342
Polymers46,6342
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-4 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.290, 108.037, 117.808
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 41667.219 Da / Num. of mol.: 1 / Fragment: UNP residues 62-411
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/peptide Chromosome-associated kinesin KIF4A / Chromokinesin-A


Mass: 4966.556 Da / Num. of mol.: 1 / Fragment: C-terminal peptide (UNP residues 1192-1232)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF4A, KIF4 / Production host: Escherichia coli (E. coli) / References: UniProt: O95239
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.64 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.75
Details: 0.1 M HEPES, pH 7.75, 0.8 M lithium chloride, 8% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.148→39.52 Å / Num. obs: 11932 / % possible obs: 96.6 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.113 / Net I/σ(I): 11.5
Reflection shellResolution: 3.148→3.36 Å / Redundancy: 7.7 % / Num. unique obs: 1801 / CC1/2: 0.73 / % possible all: 83.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5K6S

5k6s


Resolution: 3.15→39.518 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.18
RfactorNum. reflection% reflection
Rfree0.2312 581 4.9 %
Rwork0.2154 --
obs0.2162 11868 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→39.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 0 7 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032881
X-RAY DIFFRACTIONf_angle_d0.6523909
X-RAY DIFFRACTIONf_dihedral_angle_d14.9861744
X-RAY DIFFRACTIONf_chiral_restr0.04429
X-RAY DIFFRACTIONf_plane_restr0.006497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.46430.34361410.29762456X-RAY DIFFRACTION86
3.4643-3.96510.27711440.24032879X-RAY DIFFRACTION100
3.9651-4.99410.23151460.21762903X-RAY DIFFRACTION99
4.9941-39.5180.19591500.19193049X-RAY DIFFRACTION99

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