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- PDB-9gsu: Structure of PP1-Neurabin bound to 4E-BP1. -

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Basic information

Entry
Database: PDB / ID: 9gsu
TitleStructure of PP1-Neurabin bound to 4E-BP1.
Components
  • Neurabin-1
  • Serine/threonine-protein phosphatase
KeywordsHYDROLASE / PP1 / neurabin / 4EBP1
Function / homology
Function and homology information


cortical actin cytoskeleton / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / actin filament organization / filopodium / modulation of chemical synaptic transmission / calcium-mediated signaling / neuron projection development / actin filament binding ...cortical actin cytoskeleton / protein serine/threonine phosphatase activity / glycogen metabolic process / protein-serine/threonine phosphatase / actin filament organization / filopodium / modulation of chemical synaptic transmission / calcium-mediated signaling / neuron projection development / actin filament binding / actin cytoskeleton / dendritic spine / postsynaptic density / cell division / dendrite / nucleus / cytoplasm
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / 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 ...Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / 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 / SAM domain (Sterile alpha motif) / Metallo-dependent phosphatase-like / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase / Neurabin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsMouilleron, S. / Treisman, R. / Fedoryshchak, R. / Elbouri, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: Identification of the 4E-BPs as substrates for the Neurabin/Spinophilin PP1 holoenzyme shows how PIPs can determine PP1 substrate specificity
Authors: mouilleron, S. / Treisman, R. / Fedoryshchak, R. / Elbouri, K.
History
DepositionSep 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase
C: Neurabin-1
D: Serine/threonine-protein phosphatase
E: Neurabin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,3668
Polymers115,1464
Non-polymers2204
Water36020
1
A: Serine/threonine-protein phosphatase
C: Neurabin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6834
Polymers57,5732
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-41 kcal/mol
Surface area18240 Å2
2
D: Serine/threonine-protein phosphatase
E: Neurabin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6834
Polymers57,5732
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-29 kcal/mol
Surface area14630 Å2
Unit cell
Length a, b, c (Å)104.955, 130.647, 156.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Serine/threonine-protein phosphatase


Mass: 38167.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8C3UBZ3, protein-serine/threonine phosphatase
#2: Protein Neurabin-1 / Neurabin-I / Neural tissue-specific F-actin-binding protein I / Protein phosphatase 1 regulatory subunit 9A


Mass: 19405.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R9A, KIAA1222 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULJ8
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6000, 0.2M MgCl2, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→52.48 Å / Num. obs: 44376 / % possible obs: 98.91 % / Redundancy: 27.2 % / Biso Wilson estimate: 42.44 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.29
Reflection shellResolution: 2.35→2.42 Å / Num. unique obs: 3023 / CC1/2: 0.28

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5058refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→52.48 Å / SU ML: 0.4048 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2732
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2812 1996 4.53 %
Rwork0.2419 42023 -
obs0.2436 44019 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.04 Å2
Refinement stepCycle: LAST / Resolution: 2.36→52.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6151 0 4 20 6175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00386287
X-RAY DIFFRACTIONf_angle_d0.59728516
X-RAY DIFFRACTIONf_chiral_restr0.0423937
X-RAY DIFFRACTIONf_plane_restr0.00511117
X-RAY DIFFRACTIONf_dihedral_angle_d18.10132299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.420.32441310.3652758X-RAY DIFFRACTION91.66
2.42-2.480.38781390.35642931X-RAY DIFFRACTION97.96
2.48-2.560.40391410.3272963X-RAY DIFFRACTION98.79
2.56-2.640.36461420.32162988X-RAY DIFFRACTION99.46
2.64-2.730.3551410.31342991X-RAY DIFFRACTION99.46
2.73-2.840.35961420.29913008X-RAY DIFFRACTION99.49
2.84-2.970.35241420.28792984X-RAY DIFFRACTION99.59
2.97-3.130.34141440.29333014X-RAY DIFFRACTION99.72
3.13-3.320.31851430.25423014X-RAY DIFFRACTION99.81
3.32-3.580.25781430.23832999X-RAY DIFFRACTION99.46
3.58-3.940.27861450.22323049X-RAY DIFFRACTION99.78
3.94-4.510.21841450.17853046X-RAY DIFFRACTION99.87
4.51-5.680.23771460.19733094X-RAY DIFFRACTION99.91
5.68-52.480.24321520.22993184X-RAY DIFFRACTION99.61

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