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- PDB-6ghm: Structure of PP1 alpha phosphatase bound to ASPP2 -

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Basic information

Entry
Database: PDB / ID: 6ghm
TitleStructure of PP1 alpha phosphatase bound to ASPP2
Components
  • Apoptosis-stimulating of p53 protein 2
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / Phosphatase / PP1 / ASPP2
Function / homology
Function and homology information


regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress ...regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatase activity / negative regulation of cell cycle / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of execution phase of apoptosis / NF-kappaB binding / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / lung development / Downregulation of TGF-beta receptor signaling / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / SH3 domain binding / response to lead ion / p53 binding / : / cell junction / presynapse / perikaryon / dendritic spine / protein stabilization / iron ion binding / cell division / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / protein homodimerization activity / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / : / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase ...: / : / : / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Ankyrin repeat / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Ankyrin repeat-containing domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / SH3 Domains / Metallo-dependent phosphatase-like / Ankyrin repeat / SH3 domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / Ubiquitin-like domain superfamily / Roll / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Apoptosis-stimulating of p53 protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMouilleron, S. / Bertran, T.M. / Tapon, N. / Zhou, Y.
CitationJournal: Nat Commun / Year: 2019
Title: ASPP proteins discriminate between PP1 catalytic subunits through their SH3 domain and the PP1 C-tail.
Authors: Bertran, M.T. / Mouilleron, S. / Zhou, Y. / Bajaj, R. / Uliana, F. / Kumar, G.S. / van Drogen, A. / Lee, R. / Banerjee, J.J. / Hauri, S. / O'Reilly, N. / Gstaiger, M. / Page, R. / Peti, W. / Tapon, N.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Apoptosis-stimulating of p53 protein 2
D: Apoptosis-stimulating of p53 protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,58930
Polymers123,0124
Non-polymers2,57726
Water4,414245
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Apoptosis-stimulating of p53 protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,01118
Polymers61,5062
Non-polymers1,50516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint7 kcal/mol
Surface area20780 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Apoptosis-stimulating of p53 protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,57812
Polymers61,5062
Non-polymers1,07210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint9 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.840, 81.624, 87.966
Angle α, β, γ (deg.)91.06, 91.84, 103.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 37349.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Apoptosis-stimulating of p53 protein 2 / Bcl2-binding protein / Bbp / Renal carcinoma antigen NY-REN-51 / Tumor suppressor p53-binding ...Bcl2-binding protein / Bbp / Renal carcinoma antigen NY-REN-51 / Tumor suppressor p53-binding protein 2 / p53BP2


Mass: 24156.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP2, ASPP2, BBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q13625

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Non-polymers , 5 types, 271 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.5 16 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→59 Å / Num. obs: 68468 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.96 / Rpim(I) all: 0.12 / Net I/σ(I): 4.3
Reflection shellResolution: 2.15→2.2 Å / CC1/2: 0.58 / Rpim(I) all: 0.49

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2.15→59.647 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2145 3477 5.08 %
Rwork0.1769 --
obs0.1788 68457 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→59.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7822 0 154 245 8221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068182
X-RAY DIFFRACTIONf_angle_d0.74711080
X-RAY DIFFRACTIONf_dihedral_angle_d9.2495993
X-RAY DIFFRACTIONf_chiral_restr0.0441207
X-RAY DIFFRACTIONf_plane_restr0.0041431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17950.29711270.26782506X-RAY DIFFRACTION97
2.1795-2.21060.28851300.25432599X-RAY DIFFRACTION98
2.2106-2.24360.32271400.24592586X-RAY DIFFRACTION98
2.2436-2.27870.28251490.2392495X-RAY DIFFRACTION99
2.2787-2.3160.2861410.22842595X-RAY DIFFRACTION99
2.316-2.3560.25321340.22242622X-RAY DIFFRACTION99
2.356-2.39880.2911280.22172624X-RAY DIFFRACTION100
2.3988-2.4450.25941360.21552605X-RAY DIFFRACTION100
2.445-2.49490.29081280.212597X-RAY DIFFRACTION100
2.4949-2.54910.25871470.20082637X-RAY DIFFRACTION100
2.5491-2.60840.25921480.20652609X-RAY DIFFRACTION100
2.6084-2.67360.24791480.19842575X-RAY DIFFRACTION100
2.6736-2.74590.24651560.17812641X-RAY DIFFRACTION100
2.7459-2.82670.26091420.17732578X-RAY DIFFRACTION100
2.8267-2.9180.1931230.17262656X-RAY DIFFRACTION100
2.918-3.02230.2041350.16262578X-RAY DIFFRACTION100
3.0223-3.14330.23231430.17022635X-RAY DIFFRACTION100
3.1433-3.28630.22581200.17272601X-RAY DIFFRACTION100
3.2863-3.45950.20491370.16172613X-RAY DIFFRACTION100
3.4595-3.67630.19121570.15732587X-RAY DIFFRACTION100
3.6763-3.96010.20651760.15422591X-RAY DIFFRACTION100
3.9601-4.35850.16271360.1442612X-RAY DIFFRACTION100
4.3585-4.98890.17361260.1472601X-RAY DIFFRACTION100
4.9889-6.28440.20951380.18712628X-RAY DIFFRACTION100
6.2844-59.66950.18441320.18332609X-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)
10.03840.0150.0240.0257-0.02150.0299-0.0418-0.30340.07080.1821-0.2234-0.0782-0.25740.3479-0.00030.3998-0.0510.0040.3490.05740.4541-9.9015-3.0184-48.1024
21.01930.5750.67211.94430.17781.13280.0716-0.0069-0.1198-0.0569-0.0718-0.2299-0.0621-0.0477-0.00110.21620.00550.03390.2720.02460.3287-23.7343-20.8376-52.2488
30.05810.03850.03380.0987-0.09150.097-0.1793-0.13530.0392-0.10410.07170.2131-0.22910.24930.00270.4907-0.07860.01740.46250.04210.3015-19.9493-12.0826-78.7073
40.022-0.031-0.00740.07560.01250.00780.31270.2129-0.3197-0.2239-0.14810.08880.21050.1344-0.00020.43310.05370.05040.3280.05250.618-32.363-69.1993-137.5925
51.0871-0.2742-0.40731.5359-0.01340.820.0682-0.03830.1103-0.1084-0.0606-0.0668-0.0172-0.043800.2505-0.013-0.03190.2736-0.01530.3128-45.0073-50.9043-133.5029
60.1084-0.1505-0.04760.0785-0.07110.2931-0.1464-0.1610.02290.24590.14150.14330.12420.04390.0030.36770.0366-0.04290.4408-0.03750.3435-44.1945-55.319-113.2897
70.06950.01740.123-0.00430.0540.1420.0286-0.1444-0.36370.2820.14250.32070.2388-0.02640.00150.6559-0.01070.01310.5637-0.04050.4401-55.8134-54.7709-105.5677
80.12360.05540.13970.0662-0.06130.3565-0.15520.0467-0.08910.07390.234-0.02380.18640.203600.69820.0281-0.01520.5714-0.05910.3899-44.1191-50.025-92.562
90.14710.08810.02640.0835-0.01120.0644-0.0350.21740.0179-0.0153-0.1583-0.1436-0.04440.5630.00080.7625-0.0109-0.0610.7164-0.05980.4074-35.5433-40.6331-87.1804
10-0.00560.02360.04250.0616-0.01710.09680.0675-0.2466-0.53150.06140.04280.11410.24920.06650.00011.02950.1559-0.0730.65020.01290.5799-39.0229-63.1638-78.0205
110.023-0.01460.00740.02470.01450.021-0.05250.0981-0.1473-0.0472-0.07250.13970.02460.10480.00010.73740.1028-0.02950.90950.01760.4351-31.1575-58.613-73.6263
120.04070.0778-0.06750.1314-0.14830.1175-0.20890.09920.21710.08930.25010.04950.43680.35460.00090.89570.1661-0.0020.6516-0.02320.4176-38.3911-61.2924-76.6863
130.0478-0.0403-0.02010.0235-0.03070.069-0.00390.18470.2378-0.15610.0660.01470.0358-0.24950.00020.54480.0560.01460.4782-0.01970.339-35.7073-20.7935-77.9735
140.04780.0259-0.06060.0511-0.00510.12240.0851-0.12640.2528-0.20480.174-0.1628-0.1463-0.02980.00010.6620.01490.05970.5507-0.0340.3493-25.2283-20.7041-87.1282
150.0389-0.0359-0.04660.02490.03360.0431-0.30530.184-0.20860.13260.1201-0.00210.23510.03860.0010.75460.05710.06140.5728-0.01150.3362-20.7278-29.1511-94.5706
160.1257-0.13350.02820.13720.04850.07610.2438-0.06830.2338-0.044-0.1125-0.62740.1740.383100.65450.03660.12650.5956-0.03780.4893-11.343-29.6301-95.9284
170.0426-0.03630.06650.0363-0.05890.1303-0.02920.320.15570.13820.1339-0.14510.00130.002-00.8682-0.08710.11830.58440.06720.5148-15.9478-12.2525-107.4706
180.00460.00540.01420.02350.01640.0439-0.2951-0.16870.0445-0.1220.05410.04930.104-0.2031-0.00010.6755-0.03170.06520.74280.03140.5077-8.9809-17.2206-111.8864
190.06-0.0239-0.04650.0472-0.08380.0948-0.25640.2629-0.12540.12730.21720.2014-0.25910.16030.00020.7698-0.1005-0.00490.72750.01620.5104-16.1451-14.1191-108.2918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 324 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 31 )
5X-RAY DIFFRACTION5chain 'B' and (resid 32 through 254 )
6X-RAY DIFFRACTION6chain 'B' and (resid 255 through 324 )
7X-RAY DIFFRACTION7chain 'C' and (resid 920 through 961 )
8X-RAY DIFFRACTION8chain 'C' and (resid 962 through 1028 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1029 through 1053 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1054 through 1082 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1083 through 1096 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1097 through 1121 )
13X-RAY DIFFRACTION13chain 'D' and (resid 920 through 948 )
14X-RAY DIFFRACTION14chain 'D' and (resid 949 through 994 )
15X-RAY DIFFRACTION15chain 'D' and (resid 995 through 1014 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1015 through 1053 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1054 through 1082 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1083 through 1096 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1097 through 1122 )

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