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- PDB-6zeg: Structure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IR... -

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Basic information

Entry
Database: PDB / ID: 6zeg
TitleStructure of PP1-IRSp53 chimera [PP1(7-304) + linker (G/S)x9 + IRSp53(449-465)] bound to Phactr1 (516-580)
Components
  • Phosphatase and actin regulator
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2
KeywordsHYDROLASE / PP1 / Phosphatase / Phactr / RPEL
Function / homology
Function and homology information


neuron projection branch point / dendritic spine cytoplasm / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / dendrite arborization / actin crosslink formation / plasma membrane organization / RNA polymerase II promoter clearance ...neuron projection branch point / dendritic spine cytoplasm / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / dendrite arborization / actin crosslink formation / plasma membrane organization / RNA polymerase II promoter clearance / glycogen granule / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress / cytoskeletal anchor activity / positive regulation of dendritic spine morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein localization to synapse / cellular response to L-glutamate / neuron projection terminus / regulation of neuron migration / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization / proline-rich region binding / dephosphorylation / regulation of canonical Wnt signaling pathway / protein phosphatase inhibitor activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / stress fiber assembly / protein-serine/threonine phosphatase / Triglyceride catabolism / entrainment of circadian clock by photoperiod / positive regulation of actin filament polymerization / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / dendrite development / phosphatase activity / telomere maintenance in response to DNA damage / actin filament bundle assembly / phosphoprotein phosphatase activity / CDC42 GTPase cycle / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / excitatory synapse / DARPP-32 events / positive regulation of excitatory postsynaptic potential / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / postsynaptic cytosol / positive regulation of glycogen biosynthetic process / postsynaptic density, intracellular component / ribonucleoprotein complex binding / protein dephosphorylation / presynaptic cytosol / ruffle / RAC1 GTPase cycle / axonogenesis / secretory granule / cellular response to epidermal growth factor stimulus / Downregulation of TGF-beta receptor signaling / transcription coregulator binding / dendritic shaft / PDZ domain binding / filopodium / adherens junction / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / cell motility / positive regulation of transcription elongation by RNA polymerase II / lung development / circadian regulation of gene expression / synaptic membrane / response to lead ion / regulation of circadian rhythm / cerebral cortex development / regulation of synaptic plasticity / Regulation of actin dynamics for phagocytic cup formation / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / : / insulin receptor signaling pathway / lamellipodium / regulation of cell shape / presynapse / actin binding / actin cytoskeleton organization / scaffold protein binding / dendritic spine / perikaryon / microtubule / protein stabilization / iron ion binding / cell division / neuronal cell body / synapse / nucleolus / glutamatergic synapse / extracellular exosome
Similarity search - Function
I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD domain profile. ...I-BAR domain containing protein IRSp53 / IRSp53, SH3 domain / I-BAR domain containing protein IRSp53/IRTKS/Pinkbar / RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / IMD/I-BAR domain / IRSp53/MIM homology domain / IMD 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 / AH/BAR domain superfamily / Variant SH3 domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15,18-HEXAOXAICOSANE / : / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Phosphatase and actin regulator / Phosphatase and actin regulator 1 / BAR/IMD domain-containing adapter protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 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,Brain-specific angiogenesis inhibitor 1-associated protein 2
C: Phosphatase and actin regulator
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2
D: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,76214
Polymers91,8724
Non-polymers89010
Water15,205844
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2
C: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2036
Polymers45,9362
Non-polymers2674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-42 kcal/mol
Surface area16240 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Brain-specific angiogenesis inhibitor 1-associated protein 2
D: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5598
Polymers45,9362
Non-polymers6236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-38 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.616, 122.394, 69.097
Angle α, β, γ (deg.)90.000, 92.219, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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,Brain-specific angiogenesis inhibitor 1-associated protein 2 / PP-1A / Protein BAP2 / Fas ligand-associated factor 3 / FLAF3 / Insulin receptor substrate p53/p58 ...PP-1A / Protein BAP2 / Fas ligand-associated factor 3 / FLAF3 / Insulin receptor substrate p53/p58 / IRSp53/58 / Insulin receptor substrate protein of 53 kDa / Insulin receptor substrate p53


Mass: 37678.723 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, BAIAP2 / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, UniProt: Q9UQB8, 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 , 5 types, 854 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-16P / 3,6,9,12,15,18-HEXAOXAICOSANE


Mass: 294.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) polyethylene glycol 3350, 0.2 M KSCN and 0.1 M BIS-Tris propane pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.09→37.18 Å / Num. obs: 332381 / % possible obs: 99.29 % / Redundancy: 2 % / Biso Wilson estimate: 10.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Rpim(I) all: 0.018 / Rrim(I) all: 0.026 / Net I/σ(I): 15.41
Reflection shellResolution: 1.09→1.13 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 62356 / CC1/2: 0.654 / Rpim(I) all: 0.44 / Rrim(I) all: 0.623

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Processing

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

4mov


Resolution: 1.09→37.18 Å / SU ML: 0.0823 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.2494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1403 16711 5.03 %
Rwork0.1195 315670 -
obs0.1206 332381 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.27 Å2
Refinement stepCycle: LAST / Resolution: 1.09→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6003 0 42 844 6889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00976555
X-RAY DIFFRACTIONf_angle_d1.17478920
X-RAY DIFFRACTIONf_chiral_restr0.0927961
X-RAY DIFFRACTIONf_plane_restr0.0081173
X-RAY DIFFRACTIONf_dihedral_angle_d23.14112535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.10.26944970.26249205X-RAY DIFFRACTION87.02
1.1-1.110.25495290.23149932X-RAY DIFFRACTION93.34
1.11-1.130.22614890.209610292X-RAY DIFFRACTION97.12
1.13-1.140.22075380.186310471X-RAY DIFFRACTION99.14
1.14-1.160.17995520.156810681X-RAY DIFFRACTION99.91
1.16-1.170.16465670.145310482X-RAY DIFFRACTION99.93
1.17-1.190.16535450.135310645X-RAY DIFFRACTION99.9
1.19-1.210.15845670.132810544X-RAY DIFFRACTION99.88
1.21-1.230.15235560.124810567X-RAY DIFFRACTION99.85
1.23-1.250.14235650.118410643X-RAY DIFFRACTION99.9
1.25-1.270.14945610.116710512X-RAY DIFFRACTION99.94
1.27-1.290.14455710.111710607X-RAY DIFFRACTION99.9
1.29-1.320.13835090.109410660X-RAY DIFFRACTION99.93
1.32-1.340.13075380.106710580X-RAY DIFFRACTION99.94
1.34-1.370.13155440.103810587X-RAY DIFFRACTION99.94
1.37-1.40.12655400.096910624X-RAY DIFFRACTION99.97
1.4-1.440.11715670.096810595X-RAY DIFFRACTION99.94
1.44-1.480.12515840.094410627X-RAY DIFFRACTION99.96
1.48-1.520.10886070.087810497X-RAY DIFFRACTION99.99
1.52-1.570.11015910.08910615X-RAY DIFFRACTION99.96
1.57-1.630.11435800.089910604X-RAY DIFFRACTION99.99
1.63-1.690.11535840.094210569X-RAY DIFFRACTION99.96
1.69-1.770.13035590.101310572X-RAY DIFFRACTION99.99
1.77-1.860.11355890.101510622X-RAY DIFFRACTION100
1.86-1.980.13325560.10810616X-RAY DIFFRACTION100
1.98-2.130.13255390.111110650X-RAY DIFFRACTION100
2.13-2.350.13815530.114910645X-RAY DIFFRACTION100
2.35-2.690.1485420.126310676X-RAY DIFFRACTION99.99
2.69-3.380.15796350.132310575X-RAY DIFFRACTION100
3.38-37.180.1355570.128510775X-RAY DIFFRACTION99.96

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