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- PDB-7qm2: Crystal structure of the PP1/PTG/beta-cyclodextrin ternary complex -

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Basic information

Entry
Database: PDB / ID: 7qm2
TitleCrystal structure of the PP1/PTG/beta-cyclodextrin ternary complex
Components
  • Protein phosphatase 1 regulatory subunit 3C
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / phosphatase / carbohydrate binding
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 / entrainment of circadian clock by photoperiod / Triglyceride catabolism / 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 / dendritic spine / molecular adaptor activity / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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
beta-cyclodextrin / 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: 2.685 Å
AuthorsSemrau, M.S. / Storici, P. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Other governmentUniversity of Trento - Starting Grant 2020 Italy
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 20, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Protein phosphatase 1 regulatory subunit 3C
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7106
Polymers114,4044
Non-polymers2,3062
Water34219
1
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)58,3553
Polymers57,2022
Non-polymers1,1531
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Protein phosphatase 1 regulatory subunit 3C

hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3553
Polymers57,2022
Non-polymers1,1531
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
Unit cell
Length a, b, c (Å)153.600, 153.600, 285.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12(chain B and (resid 83 through 206 or resid 211 through 259))
22(chain D and resid 83 through 259)

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
111LEULEUALAALAchain AAA7 - 2996 - 298
211LEULEUALAALAchain CCC7 - 2996 - 298
112LYSLYSASNASN(chain B and (resid 83 through 206 or resid 211 through 259))BB83 - 20619 - 142
122THRTHRVALVAL(chain B and (resid 83 through 206 or resid 211 through 259))BB211 - 259147 - 195
212LYSLYSVALVAL(chain D and resid 83 through 259)DD83 - 25919 - 195

NCS ensembles :
ID
1
2

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Components

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


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: phosphatase domain (residues 7-300)
Mutation: First residues 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P62136, protein-serine/threonine phosphatase
#2: Protein Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 5 / PP1 subunit R5 / Protein targeting to glycogen / PTG


Mass: 23039.740 Da / Num. of mol.: 2 / Fragment: residues 70-264)
Mutation: First residues GPLGS derive from the expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R3C, PPP1R5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UQK1
#3: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium acetate, 1 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.685→120.585 Å / Num. obs: 36706 / % possible obs: 66.3 % / Redundancy: 32 % / CC1/2: 0.997 / Rmerge(I) obs: 0.363 / Rpim(I) all: 0.09 / Net I/σ(I): 13.3
Reflection shellResolution: 2.685→2.883 Å / Redundancy: 33.9 % / Num. unique obs: 1837 / CC1/2: 0.422 / % possible all: 18.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata scaling
PHASERphasing
PHENIX1.11.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QF7, 7QFB

7qf7

7qfb


Resolution: 2.685→52.294 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2127 1835 5 %
Rwork0.177 34869 -
obs0.1789 36704 65.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.67 Å2 / Biso mean: 62.5772 Å2 / Biso min: 27.81 Å2
Refinement stepCycle: final / Resolution: 2.685→52.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 154 19 7413
Biso mean--76.56 50.57 -
Num. residues----895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017570
X-RAY DIFFRACTIONf_angle_d1.22910259
X-RAY DIFFRACTIONf_chiral_restr0.0691166
X-RAY DIFFRACTIONf_plane_restr0.0061292
X-RAY DIFFRACTIONf_dihedral_angle_d17.1814403
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2717X-RAY DIFFRACTION13.024TORSIONAL
12C2717X-RAY DIFFRACTION13.024TORSIONAL
21B1479X-RAY DIFFRACTION13.024TORSIONAL
22D1479X-RAY DIFFRACTION13.024TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6855-2.75810.3515170.31182937
2.7581-2.83920.4493530.314991423
2.8392-2.93080.3435650.2918117930
2.9308-3.03560.2705750.2931156139
3.0356-3.15710.33421020.2581183146
3.1571-3.30080.28821130.2427219554
3.3008-3.47480.2761430.2186279368
3.4748-3.69240.26761670.1936331481
3.6924-3.97740.19882020.1785388595
3.9774-4.37750.19492250.14534125100
4.3775-5.01050.15242080.12734150100
5.0105-6.3110.20422140.16694202100
6.311-52.2940.20232510.1854427100
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)
16.09080.47210.76171.45550.60522.85510.2079-0.18540.09270.04770.4624-0.56360.02130.70370.54870.07610.12890.0420.8630.00620.558925.1573-65.6347-0.6444
25.0806-5.65590.87877.7329-2.15051.8177-0.2164-0.8910.08650.57460.4669-0.5804-0.05060.2078-0.21050.09440.028-0.07920.8062-0.02260.417616.8971-56.62527.5101
33.3805-0.58550.03076.65871.47542.48110.10880.9264-0.0199-0.44540.1229-0.26190.04120.0141-0.22860.16060.07540.0480.80640.10140.367213.812-56.101-10.532
42.80290.49070.23382.1536-0.73772.09330.18990.152-0.10170.0178-0.0130.0071-0.0425-0.0207-0.17880.13150.05610.0240.60420.00960.31139.5438-58.0315-0.3463
55.49771.93912.06763.65830.73633.4352-0.05310.1070.4167-0.0857-0.20880.2849-0.5259-0.49240.27330.19660.09790.05710.70660.08560.3656-4.0735-46.1061-3.6238
65.4392.8786-0.95953.9266-2.04843.56060.3060.86940.1179-0.2722-0.3360.4313-0.3465-0.4251-0.0970.28190.18380.02730.88270.12690.3323-8.6944-44.7119-12.0706
72.4031-0.5615-0.44744.1836-0.86573.11280.10410.9662-0.0209-0.61120.1191-0.04720.10120.1552-0.14830.31670.08980.08891.15450.06630.21155.3469-53.3425-19.9076
81.44561.4503-0.14596.81450.09095.7030.19760.76590.7944-2.02290.2825-0.9952-0.54680.0651-0.59760.75060.07690.26061.27820.39560.674910.8338-42.4716-27.7241
91.12570.7760.84511.16330.39770.6845-0.01130.9704-1.0327-0.4469-0.185-0.57170.32130.56210.05180.46460.25840.23051.3408-0.13360.835518.9344-64.9046-22.4176
105.5497-4.3816-1.12464.09712.4253.92280.5323-0.51511.0595-0.399-0.4859-0.8273-0.5989-0.2551-0.3720.26480.01080.15751.0931-0.18630.652633.3703-51.3147-8.7058
111.09112.1424-2.28854.3219-4.73315.24280.4585-0.0977-0.14081.0023-0.5511-0.3266-0.97180.66270.07270.6367-0.139-0.11820.6188-0.03040.549914.6094-47.06779.2765
124.9193.3676-0.56436.49222.2877.10230.091-0.4111-0.6171-0.5234-0.53170.1555-0.3424-0.67120.28250.3626-0.1374-0.22380.71750.01560.61749.3268-57.730725.7948
137.33781.7154-1.19884.0846-1.03315.4696-0.1266-0.50040.6062-0.0314-0.05780.2664-0.99650.05240.16210.5695-0.1508-0.12430.5716-0.06570.38216.3498-46.630931.247
147.03633.86653.01472.1341.66221.3129-0.9814-0.44410.307-0.46510.10991.19850.7106-0.89320.53270.7376-0.2314-0.00121.2299-0.09010.8628-0.0856-50.966234.765
155.0637-0.1107-0.00295.0820.89266.57810.2779-0.41570.1962-0.2146-0.2621-0.0687-0.84110.4050.05050.4849-0.2481-0.18540.58760.02440.445717.6157-47.52828.854
163.8973-4.89763.05419.7082-6.7114.7119-0.29311.5985-0.5061-1.0678-0.1565-0.7004-0.25720.60690.42040.6827-0.2811-0.08860.8016-0.00680.513820.8789-51.289419.622
173.81230.55830.80262.70630.45811.82420.1375-0.2913-0.5731-0.1078-0.2140.2640.1378-0.35370.0370.0181-0.0845-0.06290.87370.04110.4248-29.857-67.793910.1557
182.56-0.03141.251.2171-0.59731.227-0.0213-0.19660.12650.0222-0.16590.0393-0.1713-0.15740.13050.0357-0.05-0.17340.85110.06890.3452-22.8121-63.62698.4286
195.4364-1.2940.20014.0956-0.22532.5208-0.0227-0.5633-0.11450.56420.0785-0.6718-0.0190.0031-0.00410.2709-0.1211-0.14820.73490.09860.4554-7.4773-65.292722.2088
203.73490.49960.35133.52371.19855.91920.2168-0.2668-0.65970.2749-0.3352-0.08030.3275-0.37370.11870.3497-0.1471-0.11410.73860.25180.6318-18.7562-80.177819.7929
212.0262-0.99720.56052.044-0.27161.21540.2991-0.555-0.23970.4142-0.29440.14870.0465-0.4381-0.01290.3778-0.1359-0.0011.0235-0.04430.4376-32.2691-69.546419.2225
227.7171-1.6013-0.85146.76692.04395.50170.2517-0.6890.89240.2282-0.0022-0.5041-0.66450.2374-0.26060.56540.13860.00190.7658-0.09470.5239-23.981-33.58237.0468
236.26041.996-1.91647.0998-2.49146.55880.1932-0.23190.85090.3290.07720.9154-0.6006-0.8537-0.32410.66750.2870.10050.8419-0.03880.5382-34.1634-36.45867.6767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 31 )A7 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 48 )A32 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 99 )A49 - 99
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 172 )A100 - 172
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 215 )A173 - 215
6X-RAY DIFFRACTION6chain 'A' and (resid 216 through 239 )A216 - 239
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 299 )A240 - 299
8X-RAY DIFFRACTION8chain 'B' and (resid 83 through 96 )B83 - 96
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 112 )B97 - 112
10X-RAY DIFFRACTION10chain 'B' and (resid 113 through 122 )B113 - 122
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 144 )B123 - 144
12X-RAY DIFFRACTION12chain 'B' and (resid 145 through 165 )B145 - 165
13X-RAY DIFFRACTION13chain 'B' and (resid 166 through 200 )B166 - 200
14X-RAY DIFFRACTION14chain 'B' and (resid 201 through 212 )B201 - 212
15X-RAY DIFFRACTION15chain 'B' and (resid 213 through 247 )B213 - 247
16X-RAY DIFFRACTION16chain 'B' and (resid 248 through 259 )B248 - 259
17X-RAY DIFFRACTION17chain 'C' and (resid 7 through 99 )C7 - 99
18X-RAY DIFFRACTION18chain 'C' and (resid 100 through 172 )C100 - 172
19X-RAY DIFFRACTION19chain 'C' and (resid 173 through 239 )C173 - 239
20X-RAY DIFFRACTION20chain 'C' and (resid 240 through 299 )C240 - 299
21X-RAY DIFFRACTION21chain 'D' and (resid 83 through 144 )D83 - 144
22X-RAY DIFFRACTION22chain 'D' and (resid 145 through 221 )D145 - 221
23X-RAY DIFFRACTION23chain 'D' and (resid 222 through 260 )D222 - 260

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