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- PDB-4i5j: PP2A PR70 Holoenzyme -

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Basic information

Entry
Database: PDB / ID: 4i5j
TitlePP2A PR70 Holoenzyme
ComponentsSerine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
KeywordsHYDROLASE / EF Hand / Phosphatase regulatory subunit / PP2A
Function / homology
Function and homology information


regulation of cell migration involved in somitogenic axis elongation / eye photoreceptor cell differentiation / somatic muscle development / protein phosphatase type 2A complex / somite development / protein phosphatase regulator activity / somitogenesis / protein dephosphorylation / negative regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process ...regulation of cell migration involved in somitogenic axis elongation / eye photoreceptor cell differentiation / somatic muscle development / protein phosphatase type 2A complex / somite development / protein phosphatase regulator activity / somitogenesis / protein dephosphorylation / negative regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / protein-macromolecule adaptor activity / calcium ion binding
Similarity search - Function
Recoverin; domain 1 - #220 / PP2A regulatory subunit B'', EF-hand domain / : / EF-hand domain / P2R3B, EF-hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Recoverin; domain 1 - #220 / PP2A regulatory subunit B'', EF-hand domain / : / EF-hand domain / P2R3B, EF-hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.091 Å
AuthorsXing, Y. / Jeffery, P.D. / Shi, Y.
CitationJournal: Cell Res. / Year: 2013
Title: Structure of the Ca(2+)-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation.
Authors: Wlodarchak, N. / Guo, F. / Satyshur, K.A. / Jiang, L. / Jeffrey, P.D. / Sun, T. / Stanevich, V. / Mumby, M.C. / Xing, Y.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 regulatory subunit B'' subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0032
Polymers33,9631
Non-polymers401
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.610, 67.610, 139.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

21A-673-

HOH

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Components

#1: Protein Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha / PP2A subunit B isoform PR72/PR130 / PP2A subunit B isoform R3 isoform / PP2A subunit B isoforms B''- ...PP2A subunit B isoform PR72/PR130 / PP2A subunit B isoform R3 isoform / PP2A subunit B isoforms B''-PR72/PR130 / PP2A subunit B isoforms B72/B130 / Serine/threonine-protein phosphatase 2A 72/130 kDa regulatory subunit B


Mass: 33963.355 Da / Num. of mol.: 1 / Fragment: PR72 (UNP RESIDUES 786-1070)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R3A, PPP2R3 / Plasmid: Pet 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06190
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50:50 (0.1 M NaH2PO4/0.1 M K2HPO4, 0.1 M MES, 2 M NaCl) 8 mg/ml protein , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2006 / Details: Si(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.09→100 Å / Num. all: 21335 / Num. obs: 21335 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.083 / Net I/σ(I): 10.9
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.442 / % possible all: 61.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
CNSrefinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.091→32.849 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1029 5.06 %Random
Rwork0.1941 ---
obs0.197 20326 90.51 %-
all-20326 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.091→32.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 1 83 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092285
X-RAY DIFFRACTIONf_angle_d1.1223104
X-RAY DIFFRACTIONf_dihedral_angle_d13.453837
X-RAY DIFFRACTIONf_chiral_restr0.081328
X-RAY DIFFRACTIONf_plane_restr0.005398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0909-2.20120.3511880.26811685X-RAY DIFFRACTION56
2.2012-2.3390.31951310.23982606X-RAY DIFFRACTION87
2.339-2.51960.28081590.20952819X-RAY DIFFRACTION95
2.5196-2.7730.24391620.20322895X-RAY DIFFRACTION97
2.773-3.1740.23971440.20533024X-RAY DIFFRACTION99
3.174-3.99780.24981780.18233042X-RAY DIFFRACTION100
3.9978-32.8530.23451670.17783226X-RAY DIFFRACTION100
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)
1-0.02220.03210.00980.03630.05560.06120.31710.3462-0.7879-0.0273-0.1588-0.34070.0302-0.28590.00060.3404-0.0236-0.01610.2911-0.13930.711257.2533-4.020822.9125
20.5684-0.0726-0.41140.43860.13770.2788-0.03820.0432-0.09190.3312-0.0523-0.04550.2019-0.0773-0.0220.31610.0041-0.02360.2140.00670.295445.30516.808836.0303
30.9207-0.0115-0.210.53320.06890.42660.13090.25560.1190.0277-0.0709-0.194-0.2723-0.17060.01340.27460.0058-0.03470.2278-0.04980.306448.561612.416729.3194
40.80250.26670.01480.4404-0.24830.61920.03740.03910.00060.0793-0.08640.0186-0.2845-0.203800.27750.0194-0.00920.3297-0.00180.266631.449315.078618.1741
51.59820.6655-0.07470.53450.26720.80950.12120.3323-0.12480.25720.07550.144-2.2623-0.68620.51120.9130.46580.02610.47330.17970.234229.552727.91273.3061
62.1357-0.2257-0.01030.30660.14580.37630.05250.09970.01170.69-0.3396-0.2457-1.48810.7298-0.07450.8341-0.0485-0.01090.38220.0450.286938.874925.15869.6952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 172 through 193 )
2X-RAY DIFFRACTION2chain 'A' and (resid 194 through 236 )
3X-RAY DIFFRACTION3chain 'A' and (resid 237 through 289 )
4X-RAY DIFFRACTION4chain 'A' and (resid 290 through 376 )
5X-RAY DIFFRACTION5chain 'A' and (resid 377 through 416 )
6X-RAY DIFFRACTION6chain 'A' and (resid 417 through 443 )

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