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- PDB-6zeh: Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (... -

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Basic information

Entry
Database: PDB / ID: 6zeh
TitleStructure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580)
Components
  • Phosphatase and actin regulator
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1
KeywordsHYDROLASE / PP1 / Phosphatase / Phactr / RPEL
Function / homology
Function and homology information


spectrin / 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 / actin filament capping ...spectrin / 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 / actin filament capping / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / actomyosin structure organization / regulation of canonical Wnt signaling pathway / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / regulation of translational initiation / protein phosphatase inhibitor activity / RHOV GTPase cycle / myosin phosphatase activity / cortical actin cytoskeleton / 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 / RHOU GTPase cycle / DARPP-32 events / Caspase-mediated cleavage of cytoskeletal proteins / ribonucleoprotein complex binding / COPI-mediated anterograde transport / dephosphorylation / NCAM signaling for neurite out-growth / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / cell projection / cell motility / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / structural constituent of cytoskeleton / cerebral cortex development / specific granule lumen / microtubule cytoskeleton / extracellular vesicle / actin filament binding / Circadian Clock / presynapse / tertiary granule lumen / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / perikaryon / dendritic spine / calmodulin binding / cadherin binding / cell cycle / cell division / intracellular membrane-bounded organelle / glutamatergic synapse / synapse / calcium ion binding / Neutrophil degranulation / nucleolus / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Alpha Spectrin, SH3 domain / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand ...RPEL repeat / RPEL repeat / RPEL repeat profile. / Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2 / Alpha Spectrin, SH3 domain / Serine-threonine protein phosphatase, N-terminal / Serine-threonine protein phosphatase N-terminal domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Spectrin repeat / Spectrin repeat / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Spectrin/alpha-actinin / Spectrin repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Spectrin alpha chain, non-erythrocytic 1 / Phosphatase and actin regulator / Phosphatase and actin regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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,Spectrin alpha chain, non-erythrocytic 1
C: Phosphatase and actin regulator
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1
D: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,13811
Polymers91,6324
Non-polymers5067
Water11,800655
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1
C: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0215
Polymers45,8162
Non-polymers2053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-45 kcal/mol
Surface area14840 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1
D: Phosphatase and actin regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1176
Polymers45,8162
Non-polymers3014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-58 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.501, 122.388, 69.343
Angle α, β, γ (deg.)90.000, 92.179, 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,Spectrin alpha chain, non-erythrocytic 1 / PP-1A / Alpha-II spectrin / Fodrin alpha chain / Spectrin / non-erythroid alpha subunit


Mass: 37558.555 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, SPTAN1, NEAS, SPTA2 / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, UniProt: Q13813, 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, 662 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: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) polyethylene glycol 3350, 0.2 M NaI 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: I24 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.3→69.29 Å / Num. obs: 196809 / % possible obs: 99.08 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1379 / Rpim(I) all: 0.058 / Rrim(I) all: 0.15 / Net I/σ(I): 5.89
Reflection shellResolution: 1.3→1.34 Å / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 123745 / CC1/2: 0.475 / Rpim(I) all: 0.75 / Rrim(I) all: 1.94

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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: 1.3→69.29 Å / SU ML: 0.123 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1693 9610 4.91 %
Rwork0.1368 186173 -
obs0.1384 195783 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.08 Å2
Refinement stepCycle: LAST / Resolution: 1.3→69.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5953 0 19 655 6627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01016270
X-RAY DIFFRACTIONf_angle_d1.14638506
X-RAY DIFFRACTIONf_chiral_restr0.0892916
X-RAY DIFFRACTIONf_plane_restr0.00811114
X-RAY DIFFRACTIONf_dihedral_angle_d24.04982360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.26622880.23955797X-RAY DIFFRACTION92.03
1.31-1.330.2633090.23116068X-RAY DIFFRACTION97.36
1.33-1.350.2623200.22486152X-RAY DIFFRACTION97.41
1.35-1.360.25993400.21476038X-RAY DIFFRACTION97.78
1.36-1.380.24593430.20166100X-RAY DIFFRACTION97.58
1.38-1.40.23923000.20176107X-RAY DIFFRACTION98.13
1.4-1.420.24353120.19516176X-RAY DIFFRACTION98.17
1.42-1.440.22753310.18286122X-RAY DIFFRACTION98.4
1.44-1.460.21313170.17266196X-RAY DIFFRACTION98.41
1.46-1.490.19993150.16246143X-RAY DIFFRACTION98.61
1.49-1.510.21393790.15396211X-RAY DIFFRACTION98.77
1.51-1.540.18363130.14246190X-RAY DIFFRACTION99.15
1.54-1.570.19633200.14156210X-RAY DIFFRACTION99.12
1.57-1.60.17152910.13636194X-RAY DIFFRACTION99.27
1.6-1.640.16323040.12776248X-RAY DIFFRACTION99.6
1.64-1.680.15943030.12886316X-RAY DIFFRACTION99.47
1.68-1.720.17133340.12716190X-RAY DIFFRACTION99.65
1.72-1.760.16113440.12826222X-RAY DIFFRACTION99.58
1.76-1.820.15823400.12256230X-RAY DIFFRACTION99.83
1.82-1.870.15573360.12036295X-RAY DIFFRACTION99.82
1.87-1.940.15943240.11826249X-RAY DIFFRACTION99.89
1.94-2.020.13843030.11456291X-RAY DIFFRACTION99.95
2.02-2.110.13643080.11136296X-RAY DIFFRACTION99.95
2.11-2.220.15982990.11286253X-RAY DIFFRACTION99.89
2.22-2.360.15143160.12016278X-RAY DIFFRACTION99.98
2.36-2.540.16233350.12146327X-RAY DIFFRACTION99.98
2.54-2.80.16522670.13246318X-RAY DIFFRACTION99.94
2.8-3.20.15843170.13346321X-RAY DIFFRACTION100
3.2-4.040.16353590.12786282X-RAY DIFFRACTION100
4.04-69.290.1523430.14476353X-RAY DIFFRACTION99.93

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