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- PDB-7qfb: Crystal structure of Protein Phosphatase 1 in complex with PP1-bi... -

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Basic information

Entry
Database: PDB / ID: 7qfb
TitleCrystal structure of Protein Phosphatase 1 in complex with PP1-binding peptide from PTG
Components
  • Protein phosphatase 1 regulatory subunit 3C
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


glycogen binding / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of glycogen biosynthetic process / 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 / cadherin binding involved in cell-cell adhesion ...glycogen binding / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of glycogen biosynthetic process / 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 / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / glycogen biosynthetic process / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / 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 / phosphatase activity / 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 glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / Myoclonic epilepsy of Lafora / Glycogen synthesis / 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 / response to lead ion / : / presynapse / protein phosphatase binding / perikaryon / molecular adaptor activity / dendritic spine / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 3B/C/D, metazoa / : / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain ...Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 3B/C/D, metazoa / : / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / 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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Protein phosphatase 1 regulatory subunit 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSemrau, M.S. / Storici, P. / Lolli, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular architecture of the glycogen- committed PP1/PTG holoenzyme.
Authors: Semrau, M.S. / Giachin, G. / Covaceuszach, S. / Cassetta, A. / Demitri, N. / Storici, P. / Lolli, G.
History
DepositionDec 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,26015
Polymers37,1262
Non-polymers1,13513
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-60 kcal/mol
Surface area13450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.382, 68.338, 119.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 34162.148 Da / Num. of mol.: 1 / Fragment: phosphatase domain (residues 7-300)
Mutation: First residue GHMGS derive from the expression tag
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/peptide Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 5 / PP1 subunit R5 / Protein targeting to glycogen / PTG


Mass: 2963.407 Da / Num. of mol.: 1 / Fragment: peptide 81-107 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQK1

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Non-polymers , 4 types, 176 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.66 Å3/Da / Density % sol: 66.38 % / Mosaicity: 0.08 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Lithium sulfate, 1.4 M sodium malonate / PH range: 6 to 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.05→68.34 Å / Num. obs: 35005 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.053 / Rrim(I) all: 0.202 / Net I/σ(I): 10 / Num. measured all: 499594 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.1114.31.5223854226960.7370.4151.5792.1100
8.94-68.3410.90.07855505080.9970.0230.08223.599.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZEG

6zeg


Resolution: 2.05→59.89 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 1791 5.13 %
Rwork0.1593 33142 -
obs0.1609 34933 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.91 Å2 / Biso mean: 38.6283 Å2 / Biso min: 17.92 Å2
Refinement stepCycle: final / Resolution: 2.05→59.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 65 163 2730
Biso mean--60.56 48.39 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062626
X-RAY DIFFRACTIONf_angle_d0.923535
X-RAY DIFFRACTIONf_chiral_restr0.054376
X-RAY DIFFRACTIONf_plane_restr0.004450
X-RAY DIFFRACTIONf_dihedral_angle_d18.0421554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.05-2.10550.27691250.23632539
2.1055-2.16740.24241370.20422494
2.1674-2.23740.21521300.19062508
2.2374-2.31730.18851430.18322512
2.3173-2.41010.22851360.18162515
2.4101-2.51980.24051390.1762528
2.5198-2.65270.22061410.16932533
2.6527-2.81890.17151460.16522509
2.8189-3.03650.20411250.16012560
3.0365-3.34210.20631290.15482556
3.3421-3.82560.1681380.13772588
3.8256-4.81950.14461420.12342587
4.8195-59.890.20131600.17262713
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)
14.53180.1072-2.35631.61432.47626.46380.0379-0.0469-0.02510.42230.0317-0.5901-0.0616-0.0329-0.17410.3312-0.0016-0.04890.2376-0.02330.35678.60331.095430.7426
24.10212.31585.76373.45242.56538.27350.2786-0.85470.30330.6465-0.34610.04410.0917-0.58960.09520.441-0.0330.04270.2704-0.03360.2698-2.7991-2.552333.1853
32.59330.74240.25113.49750.46712.90620.02720.07460.06430.0229-0.031-0.0986-0.17940.0790.01860.20110.0049-0.00640.1819-0.01670.19630.1543-7.257518.7303
42.6190.16821.76273.23660.05344.66610.038-0.26430.0580.6332-0.1731-0.10310.1021-0.16870.10310.271-0.03470.01840.19510.00240.2029-3.2926-13.867228.298
54.02150.36650.89633.73010.58525.14560.1536-0.38230.24450.2125-0.15340.5804-0.0723-0.76150.03210.1984-0.01330.06620.3588-0.02670.3312-19.2433-15.746422.4007
63.87630.53210.11272.1631-0.12943.477-0.02770.2712-0.293-0.16470.02350.13150.3231-0.2459-0.00130.20720.0087-0.03160.2179-0.04290.2267-11.5597-21.79689.9402
74.4961.0274-0.03542.5914-0.22635.34330.05150.49580.1187-0.2312-0.2951-0.58560.19750.59050.26790.2051-0.00020.02710.2578-0.0210.20682.8007-13.53246.682
83.8540.966-3.39328.91323.19674.88980.23821.44560.3733-0.8367-0.33070.7969-0.3335-0.6282-0.1110.41540.0681-0.11180.53970.07110.3498-11.0432-6.7653-3.2992
92.44150.21571.48663.88991.41281.84580.01890.26050.06480.05120.0934-0.2669-0.12040.04-0.18230.2954-0.00550.06260.55560.02960.25638.3156-11.18361.5591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 48 )A32 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 127 )A49 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 172 )A128 - 172
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 199 )A173 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 271 )A200 - 271
7X-RAY DIFFRACTION7chain 'A' and (resid 272 through 300 )A272 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 82 through 91 )B82 - 91
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 103 )B92 - 103

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