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- PDB-6zei: Structure of PP1-IRSp53 S455E chimera [PP1(7-304) + linker (G/S)x... -

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Basic information

Entry
Database: PDB / ID: 6zei
TitleStructure of PP1-IRSp53 S455E 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 / 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 / plasma membrane organization / glycogen granule / RNA polymerase II promoter clearance / actin crosslink formation / dendrite arborization ...neuron projection branch point / 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 / plasma membrane organization / glycogen granule / RNA polymerase II promoter clearance / actin crosslink formation / dendrite arborization / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / cytoskeletal anchor activity / regulation of translational initiation in response to stress / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / protein localization to synapse / regulation of neuron migration / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization / proline-rich region binding / cellular response to L-glutamate / dephosphorylation / regulation of canonical Wnt signaling pathway / dendritic spine cytoplasm / protein phosphatase inhibitor activity / glycogen metabolic process / protein dephosphorylation / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / branching morphogenesis of an epithelial tube / Triglyceride catabolism / stress fiber assembly / protein serine/threonine phosphatase activity / positive regulation of actin filament polymerization / neuron projection terminus / dendrite development / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / actin filament bundle assembly / CDC42 GTPase cycle / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / RAC3 GTPase cycle / DARPP-32 events / RHO GTPases Activate WASPs and WAVEs / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / postsynaptic cytosol / postsynaptic density, intracellular component / presynaptic cytosol / : / ruffle / phosphoprotein phosphatase activity / RAC1 GTPase cycle / excitatory synapse / lung development / axonogenesis / secretory granule / cellular response to epidermal growth factor stimulus / synaptic membrane / positive regulation of excitatory postsynaptic potential / dendritic shaft / Downregulation of TGF-beta receptor signaling / transcription coregulator binding / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / PDZ domain binding / filopodium / adherens junction / circadian regulation of gene expression / cell motility / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / regulation of synaptic plasticity / cerebral cortex development / Regulation of actin dynamics for phagocytic cup formation / response to lead ion / VEGFA-VEGFR2 Pathway / Schaffer collateral - CA1 synapse / insulin receptor signaling pathway / regulation of cell shape / lamellipodium / presynapse / actin binding / actin cytoskeleton organization / scaffold protein binding / dendritic spine / microtubule / perikaryon / 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
: / 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: 1.39 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

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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)92,64213
Polymers91,9564
Non-polymers6869
Water12,448691
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)46,3677
Polymers45,9782
Non-polymers3895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-42 kcal/mol
Surface area14770 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)46,2756
Polymers45,9782
Non-polymers2974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-39 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.795, 122.329, 69.424
Angle α, β, γ (deg.)90.000, 92.266, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 37720.758 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 , 4 types, 700 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 20% (w/v) polyethylene glycol 3350 and 0.2 M NaBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.39→69.37 Å / Num. obs: 162314 / % possible obs: 99.61 % / Redundancy: 6.5 % / Biso Wilson estimate: 16.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 12.54
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 15982 / CC1/2: 0.54 / Rpim(I) all: 0.52 / Rrim(I) all: 1.18

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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: 1.39→69.37 Å / SU ML: 0.1406 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.7329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1579 1999 1.23 %
Rwork0.1296 160191 -
obs0.1299 162190 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.7 Å2
Refinement stepCycle: LAST / Resolution: 1.39→69.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 32 691 6682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01096274
X-RAY DIFFRACTIONf_angle_d1.28668501
X-RAY DIFFRACTIONf_chiral_restr0.1009912
X-RAY DIFFRACTIONf_plane_restr0.00771112
X-RAY DIFFRACTIONf_dihedral_angle_d23.31652377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.28481430.251211221X-RAY DIFFRACTION98.13
1.42-1.460.25321360.215311367X-RAY DIFFRACTION99.1
1.46-1.510.24981480.179411361X-RAY DIFFRACTION99.33
1.51-1.550.18981380.142711381X-RAY DIFFRACTION99.45
1.55-1.610.17581500.127811477X-RAY DIFFRACTION99.6
1.61-1.670.15121400.121111414X-RAY DIFFRACTION99.73
1.67-1.750.16181370.114511458X-RAY DIFFRACTION99.84
1.75-1.840.14461480.103311466X-RAY DIFFRACTION99.97
1.84-1.960.12361400.101611490X-RAY DIFFRACTION100
1.96-2.110.13651420.103511505X-RAY DIFFRACTION99.99
2.11-2.320.15121400.107111487X-RAY DIFFRACTION100
2.32-2.660.13931480.116211490X-RAY DIFFRACTION100
2.66-3.350.13921470.132211522X-RAY DIFFRACTION99.99
3.35-69.370.1721420.14511552X-RAY DIFFRACTION99.3

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