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- PDB-6dno: Crystal structure of Protein Phosphatase 1 (PP1) bound to the mus... -

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Basic information

Entry
Database: PDB / ID: 6dno
TitleCrystal structure of Protein Phosphatase 1 (PP1) bound to the muscle glycogen-targeting subunit (Gm)
Components
  • Microcystin-LR
  • Protein phosphatase 1 regulatory subunit 3A
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsSIGNALING PROTEIN / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


protein phosphatase type 1 complex / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation ...protein phosphatase type 1 complex / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Microcystin LR / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Protein phosphatase 1 regulatory subunit 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChoy, M.S. / Kumar, G.S. / Peti, W. / Page, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)GM098482 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)NS091336 United States
CitationJournal: Sci Adv / Year: 2018
Title: Identification of the substrate recruitment mechanism of the muscle glycogen protein phosphatase 1 holoenzyme.
Authors: Kumar, G.S. / Choy, M.S. / Koveal, D.M. / Lorinsky, M.K. / Lyons, S.P. / Kettenbach, A.N. / Page, R. / Peti, W.
History
DepositionJun 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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: Protein phosphatase 1 regulatory subunit 3A
C: Microcystin-LR


Theoretical massNumber of molelcules
Total (without water)38,6293
Polymers38,6293
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-17 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.476, 65.744, 160.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-102-

HOH

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Components

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


Mass: 34162.148 Da / Num. of mol.: 1 / Fragment: residues 7-300
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 3A / Protein phosphatase 1 glycogen-associated regulatory subunit / Protein phosphatase type-1 glycogen ...Protein phosphatase 1 glycogen-associated regulatory subunit / Protein phosphatase type-1 glycogen targeting subunit / RG1


Mass: 3452.802 Da / Num. of mol.: 1 / Fragment: residues 64-93 / Source method: obtained synthetically / Source: (synth.) Oryctolagus cuniculus (rabbit) / References: UniProt: Q00756
#3: Protein/peptide Microcystin-LR / / Microcystin-LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Microcystin LR
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.6
Details: 0.4 M magnesium formate dihydrate, 0.1 M Sodium Acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.45→38.9 Å / Num. obs: 56091 / % possible obs: 98.5 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.337 / % possible all: 72.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSoct 15, 2015data reduction
Aimless0.5.17data scaling
PHENIX2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mov

4mov


Resolution: 1.45→38.9 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2680 4.78 %random selection
Rwork0.1859 ---
obs0.187 56035 98.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 71 147 2765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052698
X-RAY DIFFRACTIONf_angle_d0.9633650
X-RAY DIFFRACTIONf_dihedral_angle_d21.863988
X-RAY DIFFRACTIONf_chiral_restr0.081390
X-RAY DIFFRACTIONf_plane_restr0.004478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4504-1.47670.36091150.33032094X-RAY DIFFRACTION74
1.4767-1.50510.33311450.29362785X-RAY DIFFRACTION99
1.5051-1.53590.30191430.26792835X-RAY DIFFRACTION100
1.5359-1.56930.27441390.2642793X-RAY DIFFRACTION100
1.5693-1.60580.25411350.24952840X-RAY DIFFRACTION100
1.6058-1.64590.24971480.24082839X-RAY DIFFRACTION100
1.6459-1.69040.23511340.22732810X-RAY DIFFRACTION100
1.6904-1.74020.25251250.21552834X-RAY DIFFRACTION100
1.7402-1.79630.23681500.21172821X-RAY DIFFRACTION100
1.7963-1.86050.23191590.20722842X-RAY DIFFRACTION100
1.8605-1.9350.25291430.20232837X-RAY DIFFRACTION100
1.935-2.02310.18951440.19992826X-RAY DIFFRACTION100
2.0231-2.12970.2121510.18072828X-RAY DIFFRACTION100
2.1297-2.26320.21961640.18572818X-RAY DIFFRACTION100
2.2632-2.43790.2041300.17852879X-RAY DIFFRACTION100
2.4379-2.68320.2131280.18812864X-RAY DIFFRACTION99
2.6832-3.07130.19241140.18092893X-RAY DIFFRACTION99
3.0713-3.86890.18821610.16262905X-RAY DIFFRACTION100
3.8689-38.9290.17791520.15433012X-RAY DIFFRACTION99

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