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- PDB-1s70: Complex between protein ser/thr phosphatase-1 (delta) and the myo... -

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Basic information

Entry
Database: PDB / ID: 1s70
TitleComplex between protein ser/thr phosphatase-1 (delta) and the myosin phosphatase targeting subunit 1 (MYPT1)
Components
  • 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130)
  • Serine/threonine protein phosphatase PP1-beta (or delta) catalytic subunitSerine/threonine-specific protein kinase
KeywordsHYDROLASE / myosin phosphatase / MYPT1 / PP1 / myosin regulation / deposphorylation
Function / homology
Function and homology information


[myosin-light-chain] phosphatase / myosin-light-chain-phosphatase activity / Signaling by MRAS-complex mutants / regulation of myosin-light-chain-phosphatase activity / positive regulation of myosin-light-chain-phosphatase activity / phosphatase regulator activity / chromosome, telomeric region => GO:0000781 / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / protein phosphatase type 1 complex ...[myosin-light-chain] phosphatase / myosin-light-chain-phosphatase activity / Signaling by MRAS-complex mutants / regulation of myosin-light-chain-phosphatase activity / positive regulation of myosin-light-chain-phosphatase activity / phosphatase regulator activity / chromosome, telomeric region => GO:0000781 / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / protein phosphatase type 1 complex / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / enzyme inhibitor activity / A band / myosin phosphatase activity / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / RHO GTPases activate PAKs / phosphatase activity / regulation of cell adhesion / RHO GTPases activate PKNs / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / 14-3-3 protein binding / RAF activation / circadian regulation of gene expression / regulation of circadian rhythm / Z disc / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / cytoskeleton / cell cycle / cell division / focal adhesion / nucleolus / protein kinase binding / signal transduction / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein phosphatase 1 regulatory subunit 12A/B/C / cGMP-dependent protein kinase, interacting domain / cGMP-dependent protein kinase interacting domain / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Domain of unknown function DUF3447 / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases ...Protein phosphatase 1 regulatory subunit 12A/B/C / cGMP-dependent protein kinase, interacting domain / cGMP-dependent protein kinase interacting domain / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / Domain of unknown function DUF3447 / 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 / Ankyrin repeat-containing domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / Serine/threonine-protein phosphatase PP1-beta catalytic subunit / Serine/threonine-protein phosphatase PP1-beta catalytic subunit / Protein phosphatase 1 regulatory subunit 12A / Protein phosphatase 1 regulatory subunit 12A
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKerff, F. / Terrak, M. / Dominguez, R.
CitationJournal: Nature / Year: 2004
Title: Structural basis of protein phosphatase 1 regulation
Authors: Terrak, M. / Kerff, F. / Langsetmo, K. / Tao, T. / Dominguez, R.
History
DepositionJan 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: 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

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Assembly

Deposited unit
A: Serine/threonine protein phosphatase PP1-beta (or delta) catalytic subunit
B: 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1225
Polymers70,8622
Non-polymers2603
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-27 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.188, 75.188, 241.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Serine/threonine protein phosphatase PP1-beta (or delta) catalytic subunit / Serine/threonine-specific protein kinase / PP-1B


Mass: 37498.086 Da / Num. of mol.: 1 / Mutation: additional AGH residues at the N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CB / Plasmid: pTYB12 IMPACT / Production host: Escherichia coli (E. coli)
References: UniProt: P62140, UniProt: P62207*PLUS, protein-serine/threonine phosphatase
#2: Protein 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130)


Mass: 33363.449 Da / Num. of mol.: 1 / Fragment: N-terminal AA 1 to 299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pACYC184-T7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q90624, UniProt: Q90623*PLUS, [myosin-light-chain] phosphatase
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 5000 monomethylether, glycerol, NH4Cl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2003
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→48.7 Å / Num. all: 18135 / Num. obs: 18135 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.91 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.43 / Num. unique all: 2519 / % possible all: 65.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJM for molecule 1 and 3 ankyrin repeats from 1IHB for molecule 2

1fjm

1ihb


Resolution: 2.7→48.67 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2713055.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 927 5.1 %RANDOM
Rwork0.223 ---
obs0.223 18135 91.1 %-
all-18135 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.2046 Å2 / ksol: 0.366467 e/Å3
Displacement parametersBiso mean: 78.2 Å2
Baniso -1Baniso -2Baniso -3
1--23.22 Å20 Å20 Å2
2---23.22 Å20 Å2
3---46.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4745 0 12 227 4984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.021.5
X-RAY DIFFRACTIONc_mcangle_it7.422
X-RAY DIFFRACTIONc_scbond_it7.262
X-RAY DIFFRACTIONc_scangle_it9.672.5
LS refinement shellResolution: 2.7→2.91 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.421 151 6.2 %
Rwork0.393 2302 -
obs-2302 63.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PEG.PARAMPEG.TOP

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