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- PDB-6obu: PP1 Y134K in complex with Microcystin LR -

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Basic information

Entry
Database: PDB / ID: 6obu
TitlePP1 Y134K in complex with Microcystin LR
Components
  • Microcystin LR
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/TOXIN / phosphatase / HYDROLASE-TOXIN complex
Function / homology
Function and homology information


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 / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress ...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 / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / entrainment of circadian clock by photoperiod / Triglyceride catabolism / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / lung development / Downregulation of TGF-beta receptor signaling / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / response to lead ion / : / presynapse / perikaryon / dendritic spine / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Microcystin LR / : / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChoy, M.S. / Moon, T.M. / Bray, J.A. / Archuleta, T.L. / Shi, W. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: SDS22 selectively recognizes and traps metal-deficient inactive PP1.
Authors: Choy, M.S. / Moon, T.M. / Ravindran, R. / Bray, J.A. / Robinson, L.C. / Archuleta, T.L. / Shi, W. / Peti, W. / Tatchell, K. / Page, R.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jul 9, 2025Group: Database references / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_ref
Item: _struct_ref.db_code

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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: Microcystin LR
D: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,26317
Polymers70,2854
Non-polymers97813
Water6,161342
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
C: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,79110
Polymers35,1422
Non-polymers6488
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-19 kcal/mol
Surface area12030 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4727
Polymers35,1422
Non-polymers3305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-30 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.348, 78.362, 134.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 34128.156 Da / Num. of mol.: 2 / Fragment: UNP residues 7-300 / Mutation: Y134K
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/peptide Microcystin LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR

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Non-polymers , 5 types, 355 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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG6000, 1 M lithium chloride, 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: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→40.17 Å / Num. obs: 49637 / % possible obs: 97.3 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.9
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.925 / Num. unique obs: 2812 / CC1/2: 0.553

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MOV

4mov


Resolution: 1.95→40.17 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.73
RfactorNum. reflection% reflection
Rfree0.2019 2589 5.23 %
Rwork0.1649 --
obs0.1668 49556 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 51 342 5167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095062
X-RAY DIFFRACTIONf_angle_d0.96842
X-RAY DIFFRACTIONf_dihedral_angle_d18.0852979
X-RAY DIFFRACTIONf_chiral_restr0.05742
X-RAY DIFFRACTIONf_plane_restr0.007891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9493-1.97150.31571430.29012281X-RAY DIFFRACTION75
1.9715-1.99470.28171460.26722487X-RAY DIFFRACTION81
1.9947-2.0190.30021270.25452606X-RAY DIFFRACTION85
2.019-2.04460.31571420.24552731X-RAY DIFFRACTION88
2.0446-2.07150.23411480.24352790X-RAY DIFFRACTION92
2.0715-2.09980.27181920.23232927X-RAY DIFFRACTION95
2.0998-2.12980.26021570.21543026X-RAY DIFFRACTION98
2.1298-2.16160.25171600.19473078X-RAY DIFFRACTION100
2.1616-2.19540.23411770.193011X-RAY DIFFRACTION100
2.1954-2.23140.21891540.18363087X-RAY DIFFRACTION100
2.2314-2.26990.20741790.18333062X-RAY DIFFRACTION100
2.2699-2.31110.2221840.18583060X-RAY DIFFRACTION100
2.3111-2.35560.24091480.17493060X-RAY DIFFRACTION100
2.3556-2.40370.19441800.16453039X-RAY DIFFRACTION100
2.4037-2.45590.22961780.183036X-RAY DIFFRACTION99
2.4559-2.5130.21391590.17233097X-RAY DIFFRACTION100
2.513-2.57590.22381690.16553052X-RAY DIFFRACTION100
2.5759-2.64550.18631640.16463036X-RAY DIFFRACTION100
2.6455-2.72330.21871840.16343046X-RAY DIFFRACTION100
2.7233-2.81120.21181720.15093106X-RAY DIFFRACTION100
2.8112-2.91170.20281910.16053023X-RAY DIFFRACTION100
2.9117-3.02820.20071590.14833049X-RAY DIFFRACTION100
3.0282-3.1660.1931680.15383077X-RAY DIFFRACTION100
3.166-3.33280.17931160.14463104X-RAY DIFFRACTION100
3.3328-3.54150.18931580.13983103X-RAY DIFFRACTION100
3.5415-3.81470.16491840.143028X-RAY DIFFRACTION100
3.8147-4.19830.16051740.13793026X-RAY DIFFRACTION100
4.1983-4.80490.16251800.13263081X-RAY DIFFRACTION100
4.8049-6.05040.2151680.16763071X-RAY DIFFRACTION100
6.0504-40.18040.19121600.17083054X-RAY DIFFRACTION100

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