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- PDB-5zt0: Crystal Structure of Protein Phosphate 1 Complexed with PP1 bindi... -

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Basic information

Entry
Database: PDB / ID: 5zt0
TitleCrystal Structure of Protein Phosphate 1 Complexed with PP1 binding domain of GL
Components
  • Protein phosphatase 1 regulatory subunit 3B
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / protein phosphorylase 1 holoenzyme
Function / homology
Function and homology information


[phosphorylase] phosphatase activity / glycogen binding / protein phosphatase type 1 complex / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / DARPP-32 events / regulation of glycogen biosynthetic process / protein phosphatase regulator activity / protein phosphatase 1 binding ...[phosphorylase] phosphatase activity / glycogen binding / protein phosphatase type 1 complex / regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / DARPP-32 events / regulation of glycogen biosynthetic process / protein phosphatase regulator activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / presynapse / regulation of translation / postsynapse / perikaryon / dendritic spine / chromosome, telomeric region / neuron projection / cell cycle / cell division / neuronal cell body / glutamatergic synapse / protein-containing complex binding / nucleolus / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein phosphatase 1 regulatory subunit 3B / 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. ...Protein phosphatase 1 regulatory subunit 3B / 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
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Protein phosphatase 1 regulatory subunit 3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32042678506 Å
AuthorsYu, J. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2011CB910500 China
CitationJournal: FEBS J. / Year: 2018
Title: Structural basis for protein phosphatase 1 recruitment by glycogen-targeting subunits
Authors: Yu, J. / Deng, T. / Xiang, S.
History
DepositionMay 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
G: Protein phosphatase 1 regulatory subunit 3B
H: Protein phosphatase 1 regulatory subunit 3B
I: Protein phosphatase 1 regulatory subunit 3B
J: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,48128
Polymers235,25210
Non-polymers1,22918
Water00
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
G: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-30 kcal/mol
Surface area13400 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
I: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-29 kcal/mol
Surface area13650 Å2
MethodPISA
3
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
H: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-30 kcal/mol
Surface area13510 Å2
MethodPISA
4
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
J: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-31 kcal/mol
Surface area13400 Å2
MethodPISA
5
E: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9244
Polymers33,7201
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-21 kcal/mol
Surface area12680 Å2
MethodPISA
6
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9244
Polymers33,7201
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-21 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.530, 106.530, 187.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32

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Components

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


Mass: 33719.645 Da / Num. of mol.: 6 / Fragment: UNP residues 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp1ca, Ppp1a / Production host: Escherichia coli (E. coli)
References: UniProt: P62137, protein-serine/threonine phosphatase
#2: Protein
Protein phosphatase 1 regulatory subunit 3B


Mass: 8233.532 Da / Num. of mol.: 4 / Fragment: UNP residues 31-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XI6
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: rod shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.1M Na/K phosphate, 26%MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.41
11K, H, -L20.103
11-h,-k,l30.097
11-K, -H, -L40.39
ReflectionResolution: 3.32→92.258 Å / Num. obs: 35147 / % possible obs: 98.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 97.3634629316 Å2 / Rmerge(I) obs: 0.197 / Net I/av σ(I): 3.4 / Net I/σ(I): 6.8
Reflection shellResolution: 3.32→3.5 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.644 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5089 / CC1/2: 0.507 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PHENIX1.10.1_2155refinement
SCALA3.3.22data scaling
iMOSFLM7.2.1data reduction
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MP0

4mp0


Resolution: 3.32042678506→41.7919786749 Å / SU ML: 0.319973062552 / Cross valid method: THROUGHOUT / σ(F): 1.42921288806 / Phase error: 24.5433750059
RfactorNum. reflection% reflection
Rfree0.233151062001 1748 4.98659211502 %
Rwork0.199851525938 --
obs0.20157166675 35054 99.7808203581 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 106.693222412 Å2
Refinement stepCycle: LAST / Resolution: 3.32042678506→41.7919786749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14732 0 42 0 14774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025126818083615080
X-RAY DIFFRACTIONf_angle_d0.6125486054820362
X-RAY DIFFRACTIONf_chiral_restr0.03921647355292190
X-RAY DIFFRACTIONf_plane_restr0.002811681094952648
X-RAY DIFFRACTIONf_dihedral_angle_d12.22374803225630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3204-3.41810.2508656110291600.2141928512622819X-RAY DIFFRACTION99.966442953
3.4181-3.52840.2719145052851300.1980251027162779X-RAY DIFFRACTION100
3.5284-3.65440.2300261582031320.2017710209062773X-RAY DIFFRACTION99.9655884377
3.6544-3.80060.1834750049581500.1797422993732769X-RAY DIFFRACTION99.9657534247
3.8006-3.97350.1996157764721320.1744576302972790X-RAY DIFFRACTION99.9657885734
3.9735-4.18280.1971432846081240.1759990262882814X-RAY DIFFRACTION99.9659748214
4.1828-4.44460.2193376643611520.1719922228562772X-RAY DIFFRACTION99.9658119658
4.4446-4.78730.2180320025891320.1933463415392786X-RAY DIFFRACTION99.8631074606
4.7873-5.26820.2543327403261400.2278583969112791X-RAY DIFFRACTION99.931810433
5.2682-6.02860.2693506361660.2483210299592742X-RAY DIFFRACTION99.8283556471
6.0286-7.5880.2652793946061860.235689888352756X-RAY DIFFRACTION100
7.588-41.79530.214227877511440.1818610307442715X-RAY DIFFRACTION97.9445015416
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)
10.88150.47320.2181.48260.41131.22750.0286-0.0054-0.0269-0.0041-0.03150.0261-0.0159-0.33580.00290.1269-0.1593-0.01010.3154-0.00290.5174-5.3209-31.88790.0107
21.1299-0.27230.11711.3981-0.03881.65610.0027-0.0855-0.0464-0.09670.00530.07630.2925-0.0893-0.0080.4675-0.0277-0.01130.01120.00980.511116.7511-27.614441.4643
31.3942-0.13310.03760.65680.21491.62810.10580.0435-0.02660.0031-0.11180.04520.1615-0.08390.00610.0995-0.1307-0.00380.2349-0.03260.5484-30.339111.7204-5.1302
41.94090.47350.27651.34240.47951.81950.0639-0.06050.1436-0.0047-0.006-0.0472-0.06880.0444-0.05790.1132-0.18050.02180.2925-0.00840.497232.07-0.435215.7966
51.07060.0550.11270.5997-0.05011.2472-0.01010.12660.05590.06830.0242-0.1555-0.28210.1806-0.01420.0775-0.064-0.03220.46160.01030.535424.477-22.1614-25.8682
61.6570.1911-0.29751.6237-0.65671.48970.03630.13390.13760.1655-0.0245-0.0485-0.11140.1372-0.01180.3111-0.1744-0.00470.16730.03180.4909-6.221332.163220.8059
74.18293.1056-0.15625.230.49071.1707-0.38860.183-0.2113-0.48210.27420.4401-0.1847-0.67240.11440.3205-0.01740.08880.5197-0.04910.6883-26.6421-29.927-0.2594
86.474-1.58491.23160.7645-0.55330.4363-0.24830.11250.3377-0.20410.10250.01380.143-0.02480.14580.4065-0.1721-0.00830.453-0.05770.8698-39.4601-8.0479-5.0674
96.3506-3.44385.54891.8816-3.09595.48750.4714-0.026-0.294-0.2510.05880.16710.3798-0.4364-0.53020.545-0.19960.11520.40320.00380.9029-1.1059-40.027441.1798
101.3295-1.62150.94562.79540.48943.9729-0.036-0.01160.22260.17510.1272-0.39810.24550.2126-0.09120.3791-0.2879-0.0150.3375-0.06260.897133.449221.191216.2614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 403
2X-RAY DIFFRACTION2B7 - 403
3X-RAY DIFFRACTION3C7 - 403
4X-RAY DIFFRACTION4D7 - 403
5X-RAY DIFFRACTION5E7 - 403
6X-RAY DIFFRACTION6F7 - 403
7X-RAY DIFFRACTION7G59 - 77
8X-RAY DIFFRACTION8H59 - 77
9X-RAY DIFFRACTION9I59 - 77
10X-RAY DIFFRACTION10J59 - 77

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