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- PDB-6dcx: iASPP-PP-1c structure and targeting of p53 -

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Basic information

Entry
Database: PDB / ID: 6dcx
TitleiASPP-PP-1c structure and targeting of p53
Components
  • RelA-associated inhibitor
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHydrolase/Transcription / iASPP / ASPP2 / PP-1c / p53 / ANK repeats / RVXF motif / dephosphorylation / SH3 / Hydrolase-Transcription complex
Function / homology
Function and homology information


multicellular organismal-level homeostasis / hair cycle / embryonic camera-type eye development / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / cardiac right ventricle morphogenesis / PTW/PP1 phosphatase complex / ventricular cardiac muscle tissue development / protein phosphatase type 1 complex / glycogen granule ...multicellular organismal-level homeostasis / hair cycle / embryonic camera-type eye development / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / cardiac right ventricle morphogenesis / PTW/PP1 phosphatase complex / ventricular cardiac muscle tissue development / protein phosphatase type 1 complex / glycogen granule / regulation of translational initiation in response to stress / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / post-embryonic development / regulation of canonical Wnt signaling pathway / glycogen metabolic process / Regulation of TP53 Activity through Association with Co-factors / protein dephosphorylation / multicellular organism growth / Phosphorylation and nuclear translocation of the CRY:PER:kinase complex / Triglyceride catabolism / protein-serine/threonine phosphatase / intercellular bridge / entrainment of circadian clock by photoperiod / negative regulation of transcription elongation by RNA polymerase II / telomere maintenance in response to DNA damage / phosphatase activity / protein serine/threonine phosphatase activity / Maturation of hRSV A proteins / transition metal ion binding / positive regulation of glycogen biosynthetic process / DARPP-32 events / ribonucleoprotein complex binding / cardiac muscle contraction / positive regulation of Ras protein signal transduction / phosphoprotein phosphatase activity / Downregulation of TGF-beta receptor signaling / circadian regulation of gene expression / positive regulation of cell differentiation / adherens junction / positive regulation of transcription elongation by RNA polymerase II / negative regulation of inflammatory response / cell junction / response to lead ion / regulation of circadian rhythm / mRNA Polyadenylation / transcription corepressor activity / presynapse / dendritic spine / perikaryon / protein stabilization / cadherin binding / iron ion binding / cell division / apoptotic process / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / endoplasmic reticulum / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RelA-associated inhibitor / RelA-associated inhibitor, SH3 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 / Variant SH3 domain / Metallo-dependent phosphatases ...RelA-associated inhibitor / RelA-associated inhibitor, SH3 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 / Variant SH3 domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Ankyrin repeat-containing domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Src homology 3 domains / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 4-Layer Sandwich / Alpha Horseshoe / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / RelA-associated inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.408 Å
AuthorsGlover, J.N.M. / Zhou, Y. / Edwards, R.A.
CitationJournal: Structure / Year: 2019
Title: Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis.
Authors: Zhou, Y. / Millott, R. / Kim, H.J. / Peng, S. / Edwards, R.A. / Skene-Arnold, T. / Hammel, M. / Lees-Miller, S.P. / Tainer, J.A. / Holmes, C.F.B. / Glover, J.N.M.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: RelA-associated inhibitor
D: RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)126,8284
Polymers126,8284
Non-polymers00
Water00
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)63,4142
Polymers63,4142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-11 kcal/mol
Surface area22360 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: RelA-associated inhibitor


Theoretical massNumber of molelcules
Total (without water)63,4142
Polymers63,4142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-9 kcal/mol
Surface area22010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.462, 135.462, 165.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11(chain A and (resid 8 through 298 or resid 318 through 324))
21(chain B and (resid 8 through 298 or resid 318 through 324))
12chain C
22(chain D and resid 622 through 822)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNPROPRO(chain A and (resid 8 through 298 or resid 318 through 324))AA8 - 29817 - 307
121PROPROASNASN(chain A and (resid 8 through 298 or resid 318 through 324))AA318 - 324327 - 333
211ASNASNPROPRO(chain B and (resid 8 through 298 or resid 318 through 324))BB8 - 29817 - 307
221PROPROASNASN(chain B and (resid 8 through 298 or resid 318 through 324))BB318 - 324327 - 333
112ARGARGLYSLYSchain CCC622 - 82222 - 222
212ARGARGLYSLYS(chain D and resid 622 through 822)DD622 - 82222 - 222

NCS ensembles :
ID
1
2

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Components

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


Mass: 38473.945 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 RelA-associated inhibitor / Inhibitor of ASPP protein / Protein iASPP / NFkB-interacting protein 1 / PPP1R13B-like protein


Mass: 24939.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R13L, IASPP, NKIP1, PPP1R13BL, RAI / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WUF5

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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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Crystals of iASPP 608-828-PP-1ca complex were grown by sitting drop vapor diffusion with a reservoir solution containing 12-15% PEG6000, 0.1 M sodium citrate, pH 5.3 and were improved by ...Details: Crystals of iASPP 608-828-PP-1ca complex were grown by sitting drop vapor diffusion with a reservoir solution containing 12-15% PEG6000, 0.1 M sodium citrate, pH 5.3 and were improved by seeding by hanging vapor diffusion at room temperature.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.07808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07808 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 21616 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 91.96 Å2 / Rmerge(I) obs: 0.297 / Rpim(I) all: 0.068 / Rrim(I) all: 0.305 / Χ2: 0.994 / Net I/σ(I): 5.2 / Num. measured all: 422651
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.4-3.5219.51.74721070.6890.4031.7940.946
3.52-3.6619.71.26121150.6760.2891.2941.043
3.66-3.83201.12721180.8490.2551.1561.016
3.83-4.0320.20.87521240.9550.1980.8970.97
4.03-4.2820.20.53721330.9770.1210.5511.01
4.28-4.61200.33821250.9890.0770.3461.027
4.61-5.0819.90.25721710.9930.0590.2630.97
5.08-5.8119.60.23421620.9920.0540.240.977
5.81-7.3218.80.14722120.9970.0350.1510.961
7.32-5017.90.06123490.9990.0150.0631.022

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.41 Å48.87 Å
Translation3.41 Å48.87 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3egg and 2vge

3egg

2vge


Resolution: 3.408→48.87 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.68
RfactorNum. reflection% reflection
Rfree0.241 1112 5.16 %
Rwork0.1874 --
obs0.1902 21545 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 232.4 Å2 / Biso mean: 103.1202 Å2 / Biso min: 40.12 Å2
Refinement stepCycle: final / Resolution: 3.408→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7972 0 0 0 7972
Num. residues----1010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048159
X-RAY DIFFRACTIONf_angle_d0.68311066
X-RAY DIFFRACTIONf_chiral_restr0.0431194
X-RAY DIFFRACTIONf_plane_restr0.0051454
X-RAY DIFFRACTIONf_dihedral_angle_d12.5824847
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2975X-RAY DIFFRACTION1.701TORSIONAL
12B2975X-RAY DIFFRACTION1.701TORSIONAL
21C1870X-RAY DIFFRACTION1.701TORSIONAL
22D1870X-RAY DIFFRACTION1.701TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.408-3.56310.29631230.2572460258397
3.5631-3.75090.30221470.238824962643100
3.7509-3.98580.29131280.208625202648100
3.9858-4.29340.24311410.18225232664100
4.2934-4.72510.25741540.159325212675100
4.7251-5.40810.25491420.171125692711100
5.4081-6.81070.22371260.195226072733100
6.8107-48.8750.19451510.170127372888100
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)
16.5752-2.07751.25371.0433-1.60393.76950.61981.3917-0.7521-0.3553-0.26161.07610.5569-0.7739-0.29830.615-0.40170.07540.9426-0.26871.0329-24.538736.5889-21.6638
29.4876-5.43750.9143.508-1.32482.0829-0.36180.5467-0.55330.6655-0.7017-1.38970.86091.09290.7390.953-0.36690.23951.0275-0.19211.098-33.943340.3455-15.3347
35.5355-2.36890.15372.88550.40893.26830.60460.95570.7218-0.6548-0.2968-0.4219-0.7374-0.0874-0.30580.9662-0.20690.1151.04240.01920.7637-40.771752.5263-26.9496
45.8027-1.8433-0.84894.86841.75744.78260.55791.1836-0.4989-0.3072-0.55060.9291-0.398-0.46940.06241.14070.0509-0.27610.9086-0.22830.9878-60.251247.5171-20.918
54.2986-2.35140.89614.03791.72483.06410.64811.1439-0.2566-0.1208-0.2578-1.0521-0.65260.4213-0.2190.831-0.26190.130.94420.25321.0559-34.960515.5329-15.8327
67.49051.02620.8348.7405-0.34737.59610.92580.64210.1453-0.09830.112-1.6532-0.35550.2052-0.41710.7556-0.01150.09971.18630.13481.3267-26.51849.5324-24.2416
79.15554.2935-0.84646.73232.88444.6580.11542.0676-0.9375-1.0361-0.2401-0.5625-0.24930.5084-0.36050.79360.24790.18391.4626-0.03910.8983-27.6663.3578-33.2666
82.86750.6189-0.39375.22990.65862.33550.4192-0.1634-0.04141.2984-0.39470.91270.486-0.4523-0.04850.8370.00560.1851.1442-0.16791.1058-23.6553-8.8586-32.9181
94.18815.8045-0.81168.9830.98486.1314-0.0026-0.3715-1.4424-1.1254-1.00460.8740.7456-0.45680.49990.95010.0760.02720.8442-0.14421.5579-21.514-12.9278-43.2927
105.1163-1.25630.45973.47920.16356.2885-0.0855-0.3518-0.97320.79350.2347-0.95310.90611.5296-0.07140.85930.1076-0.141.24290.06051.1184-3.2121-9.7758-34.5805
113.13930.9206-0.81255.0682-0.0897.0086-0.1753-0.052-0.04580.66320.1335-0.63360.08920.61660.06950.5403-0.056-0.21180.587-0.05640.6016-45.24556.63775.6384
122.1394-0.4275-1.66934.5659-3.14187.8529-0.3490.03810.08440.31410.33890.14230.2296-0.7787-0.05420.4281-0.0781-0.11330.5509-0.06290.4477-56.16955.06142.6794
133.75-0.597-1.86935.2545-1.00778.19020.2820.82840.2993-0.2075-0.11990.5372-0.734-1.2437-0.29720.5365-0.014-0.03560.79270.07260.487-59.474614.1183-11.9864
144.9740.8942-1.67986.1444-1.93397.42160.19991.2810.44-0.7150.27830.60310.2219-0.7445-0.19590.82680.0213-0.13510.96620.22430.5153-56.122312.6003-20.9871
153.5582-3.73170.88146.2199-1.53997.12040.0890.6797-0.2768-0.7311-0.397-0.42680.87790.16870.24580.5173-0.14980.08430.7762-0.0520.7124-43.49554.9636-13.879
164.5933-4.4762-2.29525.50861.10222.6011-0.1504-0.4862-0.4485-0.52260.3190.2943-0.08990.8203-0.33880.4171-0.0649-0.06791.22070.06160.9453-25.0635-0.1209-14.8114
172.3574-0.17531.25692.41051.31537.0509-0.4080.2687-0.454-0.03510.2578-0.0325-0.25670.14320.10130.5405-0.1620.18630.5956-0.02110.6479-10.733350.7839-0.1949
182.9832-2.9715-0.07973.0438-0.03210.81990.2707-0.29370.6309-0.3617-0.1574-0.6553-0.12490.3063-0.03940.8309-0.2442-0.02270.8524-0.17810.9214-39.748645.7311-8.373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 622 through 649 )C622 - 649
2X-RAY DIFFRACTION2chain 'C' and (resid 650 through 662 )C650 - 662
3X-RAY DIFFRACTION3chain 'C' and (resid 663 through 754 )C663 - 754
4X-RAY DIFFRACTION4chain 'C' and (resid 755 through 822 )C755 - 822
5X-RAY DIFFRACTION5chain 'D' and (resid 608 through 637 )D608 - 637
6X-RAY DIFFRACTION6chain 'D' and (resid 638 through 662 )D638 - 662
7X-RAY DIFFRACTION7chain 'D' and (resid 663 through 681 )D663 - 681
8X-RAY DIFFRACTION8chain 'D' and (resid 682 through 740 )D682 - 740
9X-RAY DIFFRACTION9chain 'D' and (resid 741 through 754 )D741 - 754
10X-RAY DIFFRACTION10chain 'D' and (resid 755 through 822 )D755 - 822
11X-RAY DIFFRACTION11chain 'A' and (resid 8 through 127 )A8 - 127
12X-RAY DIFFRACTION12chain 'A' and (resid 128 through 172 )A128 - 172
13X-RAY DIFFRACTION13chain 'A' and (resid 173 through 215 )A173 - 215
14X-RAY DIFFRACTION14chain 'A' and (resid 216 through 239 )A216 - 239
15X-RAY DIFFRACTION15chain 'A' and (resid 240 through 285 )A240 - 285
16X-RAY DIFFRACTION16chain 'A' and (resid 286 through 324 )A286 - 324
17X-RAY DIFFRACTION17chain 'B' and (resid 8 through 285 )B8 - 285
18X-RAY DIFFRACTION18chain 'B' and (resid 286 through 328 )B286 - 328

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