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- PDB-6zef: Structure of PP1(7-300) bound to Phactr1 (516-580) at pH 5.25 -

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Basic information

Entry
Database: PDB / ID: 6zef
TitleStructure of PP1(7-300) bound to Phactr1 (516-580) at pH 5.25
Components
  • Phosphatase and actin regulator
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / PP1 / Phosphatase / Phactr / RPEL
Function / homology
Function and homology information


regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / dendrite arborization / regulation of glycogen biosynthetic process / regulation of neuron migration / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / dendrite arborization / regulation of glycogen biosynthetic process / regulation of neuron migration / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization / regulation of canonical Wnt signaling pathway / regulation of translational initiation / protein phosphatase inhibitor activity / myosin phosphatase activity / branching morphogenesis of an epithelial tube / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / stress fiber assembly / Triglyceride catabolism / Maturation of hRSV A proteins / entrainment of circadian clock by photoperiod / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / cell motility / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / cerebral cortex development / Circadian Clock / presynapse / actin binding / actin cytoskeleton organization / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / synapse / nucleolus / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / 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 / Calcineurin-like phosphoesterase domain, ApaH type ...RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Phosphatase and actin regulator / Phosphatase and actin regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMouilleron, S. / Treisman, R. / Fedoryshchak, R. / Lee, R. / Butler, A.M. / Prechova, M.
CitationJournal: Elife / Year: 2020
Title: Molecular basis for substrate specificity of the Phactr1/PP1 phosphatase holoenzyme.
Authors: Fedoryshchak, R.O. / Prechova, M. / Butler, A. / Lee, R. / O'Reilly, N. / Flynn, H.R. / Snijders, A.P. / Eder, N. / Ultanir, S. / Mouilleron, S. / Treisman, R.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Phosphatase and actin regulator
D: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,59117
Polymers84,8394
Non-polymers75213
Water4,360242
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87510
Polymers42,4192
Non-polymers4568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-38 kcal/mol
Surface area15170 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7167
Polymers42,4192
Non-polymers2965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-22 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.510, 57.550, 89.614
Angle α, β, γ (deg.)78.076, 74.673, 81.660
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 34162.148 Da / Num. of mol.: 2 / Mutation: N-terminal Vector derived sequence GHMGS
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 Phosphatase and actin regulator


Mass: 8257.345 Da / Num. of mol.: 2 / Mutation: N-terminal Vector derived sequence GPLGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHACTR1, hCG_1818446 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VY12, UniProt: Q9C0D0*PLUS

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Non-polymers , 4 types, 255 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.25
Details: 1M LiCl, 0.1 M tri-sodium citrate pH 5.25 and 10 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.94→56.05 Å / Num. obs: 65136 / % possible obs: 98.54 % / Redundancy: 8 % / Biso Wilson estimate: 30.05 Å2 / CC1/2: 0.88 / Rmerge(I) obs: 0.1329 / Rpim(I) all: 0.047 / Rrim(I) all: 0.1414 / Net I/σ(I): 9.77
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.73 / Num. unique obs: 6061 / CC1/2: 0.885 / Rpim(I) all: 0.26 / Rrim(I) all: 0.64 / % possible all: 91.97

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 1.94→56.05 Å / SU ML: 0.182 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 3131 4.81 %
Rwork0.1815 61953 -
obs0.1829 65084 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 1.94→56.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 37 242 5947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00495832
X-RAY DIFFRACTIONf_angle_d0.84147874
X-RAY DIFFRACTIONf_chiral_restr0.0465859
X-RAY DIFFRACTIONf_plane_restr0.00411024
X-RAY DIFFRACTIONf_dihedral_angle_d17.48752164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.27761300.25162475X-RAY DIFFRACTION85.44
1.97-20.2421350.21882774X-RAY DIFFRACTION97.29
2-2.040.23351580.21292875X-RAY DIFFRACTION98.89
2.04-2.070.2181490.19632758X-RAY DIFFRACTION98.78
2.07-2.110.23271330.18732802X-RAY DIFFRACTION98.92
2.11-2.160.20571240.18052922X-RAY DIFFRACTION99.58
2.16-2.20.22181560.17992788X-RAY DIFFRACTION99.86
2.2-2.260.24631320.20232836X-RAY DIFFRACTION98.7
2.26-2.310.22591670.19062784X-RAY DIFFRACTION98.93
2.31-2.370.23531460.17132893X-RAY DIFFRACTION99.7
2.37-2.440.20361450.18182788X-RAY DIFFRACTION99.8
2.44-2.520.22881440.17232898X-RAY DIFFRACTION99.93
2.52-2.610.18821340.1762853X-RAY DIFFRACTION99.93
2.61-2.720.25061170.17612880X-RAY DIFFRACTION99.97
2.72-2.840.21461440.18752737X-RAY DIFFRACTION96.03
2.84-2.990.20261520.17842859X-RAY DIFFRACTION99.9
2.99-3.180.22961340.18672883X-RAY DIFFRACTION99.97
3.18-3.420.20731610.18162826X-RAY DIFFRACTION99.97
3.42-3.770.22441360.17682846X-RAY DIFFRACTION100
3.77-4.310.19181410.16562883X-RAY DIFFRACTION100
4.31-5.430.17991480.15912759X-RAY DIFFRACTION97.71
5.43-56.050.21051450.20622834X-RAY DIFFRACTION98.94
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)
13.576605284881.233631090791.008519974872.40356937974-0.3807412919220.553855971254-0.3994778506040.4552071205560.533664870918-0.7362696185840.298393386795-0.7353594090760.1703344694590.600320914893-0.1114822230720.4116107774250.1088063616030.0861360815510.539975143245-0.1413194620210.45172602032927.93502751099.1239458375-13.6524060599
20.1893633417310.0115210929006-0.01276272171030.1058898270760.03800677742190.0309616101198-0.02807677431960.3763728900140.0874186900925-0.087095998532-0.08610052178260.2942885017790.729957900081-0.208996743031-0.002815344840020.462240611624-0.0190631492550.02296136484660.305449788799-0.02377211971260.2828274467312.82650139626.34837910497-6.43871300418
30.901751703820.002010280711140.2280981254291.458554235310.4810277796040.996889555-0.07841490643530.1542003325620.156474810134-0.04325479086430.0299872169054-0.1360271969490.0516980984430.3186731640274.56247756246E-60.222700856564-0.001045250327880.007611611955460.3253760274640.01232478031920.25419523329621.091739309317.468178526-3.72563725921
40.6084952359580.04699046705710.5078361507961.66908372856-0.2396320288881.77814275791-0.142576214274-0.03989251831550.2143553137730.2453806283330.008216763536630.0718830188909-0.224573722028-0.04734297555197.48963343764E-60.285884425535-0.00438751296055-0.009107351500730.242587948991-0.03360656604650.29999846870513.722160753127.55916855017.21119014629
50.1039262026390.0107789468532-0.02468638249220.7406016592850.4459801685980.276669722142-0.1916427021340.09339249763920.3337746413590.204717186016-0.216305840419-0.475659498713-0.3117284883560.689212186264-0.05286735368190.314987547133-0.100574095565-0.0650408758830.5488160391960.1100320737480.46570465340631.236507030326.84350294483.66568649177
63.59185552054-1.09651789802-1.379507756282.02534546976-0.08969829906230.685545954837-0.392791943586-0.600223945726-0.5008547571680.641193807460.213351286607-0.504054909478-0.3064177069970.798276659321-0.1390483543530.399269542416-0.0949835219644-0.1075434064070.588910105096-0.1205893822010.44607710724351.589201387924.671040682654.4376186695
70.112142956149-0.0319984971027-0.01263688899910.1642464609680.03460149384160.0314914197730.032097990883-0.3389635262340.2565924270080.0185373852687-0.1000361982120.384238744357-0.727008922974-0.407198803477-9.12913247449E-50.443177755855-0.00263255551645-0.02410964745150.317037697043-0.05318390305550.31270737108736.533869473827.145732840746.842662359
80.8599111284120.0433420563825-0.4669721041251.67146225795-0.1423682873612.03318323617-0.0605094506403-0.0243825151671-0.131699500442-0.0633992332295-0.00791524398487-0.0201345174669-0.04399906005580.201872094692-1.48730249014E-50.2001599389040.00912985169861-0.005218487668110.252753688258-0.006153097426940.24221024147740.011455089113.675271192440.7237649559
90.8605629441720.143524269404-0.02097864877910.05176419578340.01691671030050.0146015619385-0.114098779440.183414899709-0.531832778278-0.189015647558-0.04947139070340.3448481438480.567826581019-0.05378280621780.08007775757110.628840380981-0.01148252878930.05113287414360.260054694953-0.09232657431260.45648302576535.6058320552-1.7862382273428.8588364198
100.3704322843540.0355189198195-0.1813922025390.7521792268990.1008503703270.220317333772-0.1175317192240.0751260488233-0.199961192665-0.369320047974-0.145300556009-0.2781878414230.2664382805240.490990995152-0.1059669672990.3396269710290.1055687945510.07609107043610.3248439248670.02325370510970.36273926360347.49729098092.4503133343532.2235146746
110.1237883460690.2290866006470.1809767134480.7842682633440.5329134297970.37223803794-0.167472567599-0.0766291948428-0.230827902802-0.128119873329-0.0867906301922-0.4791408723050.0442971893920.413016303321-0.06582001779230.2931463275080.1223523628080.05743453473660.5217586985340.0852120153820.45694804047354.94715823156.7228493697537.0470818568
120.483596269735-1.16666729574-0.4885032856072.821529335891.18649179470.499734830459-0.2778702408040.02378521915930.1074637008850.870733645797-0.1767230644920.02797237107480.2734956958320.0602503431551-0.6710574874670.54924816173-0.131753573773-0.1517009823360.570456200499-0.03540844042960.30164025242328.042703938123.882545011121.8986463468
132.81948318661-0.5749925323540.9818251770841.823782729010.4826698123820.6161613157970.3181020237560.442106991165-0.0280645821186-0.340426859125-0.04580400645160.0844513311649-0.3911572256960.4849662478760.2832953959970.315487549708-0.1259381419090.02169294776340.6986739993330.1687664933480.40173993586126.131499720229.4594697-13.7611288086
140.146278357616-0.492371919754-0.2324218274882.548894966972.117617785252.382731874790.00655052438992-0.1057206956060.1570175349110.400786284316-0.1234447202810.2646970635320.396476545352-0.490991665132-0.2944004662570.281897237771-0.150456618706-0.1457522050160.5530975946630.1703425968950.58952686785-0.34695304511323.894556339-14.1563712391
150.02381202565330.0253641073752-0.01302362455850.0271843632612-0.01819034368610.164633479014-0.007566978100820.196812250699-0.03026421669030.0712589279272-0.3948906162640.0918707203153-0.03252611640460.367399856193-0.005103781876060.544907266812-0.275029243164-0.1126952015811.0252178762-0.01589773821121.015716638-4.2631214935125.69691721834.6453560541
160.1632103356780.638957839060.2453471718772.515388705250.969461373990.373877812388-0.2337757650910.0649793144079-0.115930217891-0.846082694547-0.244364560870.137031509415-0.3053220437830.135967816282-0.4103372881130.5783671549810.1213030866480.1365701978410.499792195577-0.003371305679960.33799035589551.83277350549.7587995406618.8467901006
170.343454315626-0.0955356461412-0.02960394727060.7171471291610.3072868000650.131496264090.21400953391-0.0753113233088-0.06213983799480.0466057113966-0.0471005880357-0.241508013220.10269650731-0.125232641641.274226406820.2531136242120.108108558549-0.02883569938950.9418888566050.1822672577110.40186006597456.09978420775.4145678648751.5251284091
180.09060380259510.117023681240.03706686011750.2064818027580.177628690530.316334964760.110943388124-0.264734861427-0.12204593640.2333579631710.04376596720610.139837824027-0.391390178572-0.1723418401470.0003932516214480.3406334792280.09081747703370.07500433204090.5034747419210.208540160420.51174691890326.69929908586.7228143677857.1130865539
190.07546751044920.2699245144340.02496888722291.03002451984-0.1261384682510.8259691969680.0328958765805-0.59850683550.02558116278880.212958742244-0.1505089888550.0319582652505-0.4065047045550.193232849558-0.03224177683880.4145802204050.1416655913110.04383368067390.8768696585550.002741116156060.69314754770120.09446865789.8112660645637.6305577572
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 31 )AA7 - 311 - 25
22chain 'A' and (resid 32 through 48 )AA32 - 4826 - 44
33chain 'A' and (resid 49 through 145 )AA49 - 14545 - 143
44chain 'A' and (resid 146 through 271 )AA146 - 271144 - 271
55chain 'A' and (resid 272 through 299 )AA272 - 299272 - 299
66chain 'B' and (resid 7 through 31 )BB7 - 311 - 25
77chain 'B' and (resid 32 through 48 )BB32 - 4826 - 42
88chain 'B' and (resid 49 through 216 )BB49 - 21643 - 212
99chain 'B' and (resid 217 through 238 )BB217 - 238213 - 234
1010chain 'B' and (resid 239 through 271 )BB239 - 271235 - 267
1111chain 'B' and (resid 272 through 299 )BB272 - 299268 - 295
1212chain 'C' and (resid 512 through 526 )CC512 - 5261 - 15
1313chain 'C' and (resid 527 through 546 )CC527 - 54616 - 35
1414chain 'C' and (resid 547 through 567 )CC547 - 56736 - 56
1515chain 'C' and (resid 568 through 576 )CC568 - 57657 - 65
1616chain 'D' and (resid 512 through 526 )DD512 - 5261 - 15
1717chain 'D' and (resid 527 through 540 )DD527 - 54016 - 29
1818chain 'D' and (resid 541 through 565 )DD541 - 56530 - 54
1919chain 'D' and (resid 566 through 575 )DD566 - 57555 - 64

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